Use of erbb4 as a prognostic and therapeutic marker for melanoma

ABSTRACT

Members of the protein tyrosine kinase (PTK) family are highly mutated in patients with melanoma. Described herein are novel somatic mutations in the ERBB4 gene that result in increased kinase activity, transformation ability and anchorage-independent growth. These ERBB4 mutations contribute to the tumorogenicity of melanoma. Provided is a method of predicting the prognosis of a patient with melanoma by detecting the presence or absence of a mutation in the ERBB4 gene. In some examples, the ERBB4 mutation is selected from G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbering based on SEQ ID NO: 1). Also provided are methods of selecting a patient as a candidate for treatment with an ERBB4 and/or PI3K/AKT pathway inhibitor, and a method of identifying a therapeutic agent for the treatment of a subject diagnosed with melanoma. Oligonucleotides that specifically hybridize with an ERBB4 nucleic acid molecule comprising a novel mutation are also provided.

CROSS REFERENCE TO RELATED APPLICATIONS

This is a divisional of U.S. application Ser. No. 13/128,125, filed Jul.18, 2011, which is the U.S. National Stage of International ApplicationNo. PCT/US2009/053005, filed Aug. 6, 2009, published in English underPCT Article 21(2), which claims the benefit of U.S. ProvisionalApplication No. 61/199,156, filed Nov. 12, 2008. The above-referencedapplications are herein incorporated by reference in their entirety.

FIELD

This disclosure concerns the identification of novel mutations inmembers of the protein tyrosine (PTK) family, including ERBB4, andmethods of use.

BACKGROUND

The protein tyrosine kinases (PTKs) are a family of proteins thatcatalyze phosphorylation of tyrosine residues in target proteins; PTKsplay important roles in cellular signaling. Within this large family ofproteins is the ERBB PTK family, which consists of four receptorkinases, ERBB1 (EGFR1, HER1), ERBB2 (c-Neu, HER2), ERBB3 (HER3) andERBB4 (HER4). The ERBB kinases regulate a wide range of cellularresponses, including cell proliferation, survival, migration anddifferentiation. ERBB signaling pathways are known to be altered in awide variety of cancers, which has led to the development of drugs tospecifically inhibit activity of members of this family (Junttila etal., Cancer Res. 65(4):1384-1393, 2005).

ERBB4 is a protein of approximately 180 kD and is expressed as fouralternatively spliced isoforms. Previous studies of the role of ERBB4 incancer development and prognosis have produced differing and sometimescontradictory results. For example, clinical studies of breast cancerhave linked ERBB4 expression to either a favorable or adverse clinicaloutcome, and in vitro studies have suggested that in breast cancercells, ERBB4 mediates either differentiation or tumorigenic growth(Junttila et al., Cancer Res. 65(4):1384-1393, 2005).

Cutaneous malignant melanoma is the most common fatal skin cancer(Jermal et al., CA Cancer J. Clin. 156(2):106-130, 2006; Tsao et al., N.Engl. J. of Med. 351:998-1012, 2004), and the incidence of this diseaseincreases each year. Patients diagnosed with malignant melanoma have anaverage survival time of less than 10 months. PTKs are frequentlymutated in cancer, and since they are amenable to pharmacologicinhibition (Futreal et al., Nat. Rev. Cancer 4:177-183, 2004; Sawyers,Nature 432:294-297, 2004), further analysis of the PTK gene family isneeded to provide insight into melanoma pathogenesis and to identify newtherapeutic strategies. Given the known role of PTKs in human cancer,and the disparate findings of studies of ERBB4 in cancer development, itis desirable to further evaluate ERBB4 in patients with malignantmelanoma.

SUMMARY

It is disclosed herein that members of the protein tyrosine kinasefamily, including ERBB4, are highly mutated in melanoma tumors. Analysisof several ERBB4 mutants revealed that the mutations result in increasedkinase activity of ERBB4 protein, increased transformation ability andincreased anchorage-independent growth.

Thus, provided herein is a method of predicting the prognosis of asubject diagnosed with melanoma, comprising detecting the presence orabsence of a mutation in the ERBB4 gene, wherein the presence of themutation in the ERBB4 gene predicts a poor prognosis. In someembodiments, the ERBB4 mutation is selected from one or more of G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbering based onSEQ ID NO: 1).

Also provided is a method of selecting a subject diagnosed with melanomaas a candidate for treatment with an ERBB4 inhibitor, a PI3K/AKT pathwayinhibitor, or both, comprising detecting the presence or absence of amutation in the ERBB4 gene of the subject, wherein the presence of amutation in the ERBB4 gene indicates that the subject is a candidate fortreatment with an ERBB4 inhibitor, a PI3K/AKT pathway inhibitor, orboth. In some embodiments, the method further includes administering tothe subject an ERBB4 inhibitor, a PI3K/AKT pathway inhibitor, or both.Further provided is a method of identifying a therapeutic agent for thetreatment of a subject diagnosed with melanoma, comprising screeningcandidate agents to select an agent that decreases activity of ERBB4, ordecreases activity of the PI3K/AKT pathway, thereby identifying atherapeutic agent for the treatment of a subject with melanoma. In someembodiments of the methods, the ERBB4 mutation is selected from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbering based onSEQ ID NO: 1).

Further provided are oligonucleotides that specifically hybridize withan ERBB4 nucleic acid molecule, wherein the ERBB4 nucleic acid moleculecomprises at least one mutation selected from G949A, G1354A, G1624A,C1630T, G1687A, G2506A and G2614A (numbering based on SEQ ID NO: 1).Also provided are arrays comprising one or more of such ERBB4mutant-specific oligonucleotides.

The foregoing and other features and advantages will become moreapparent from the following detailed description of several embodiments,which proceeds with reference to the accompanying figures.

BRIEF DESCRIPTION OF THE FIGURES

FIGS. 1A-1G: Distribution of mutations in ERBB4 and increased basalactivation of ERBB4 mutants. (FIG. 1A) Arrows indicate the location ofERBB4 somatic mutations found in this screen. Numbering of the ERBB4amino acid residues is based on SEQ ID NO: 2. Stars indicate ERBB4mutants evaluated for increased tyrosine kinase activity. Boxesrepresent functional domains (I, extracellular domain subregion I; II,extracellular domain subregion II; III, extracellular domain subregionIII; IV, extracellular domain subregion IV; PTK, tyrosine kinasedomain). (FIG. 1B) ERBB4 mutants have increased tyrosinephosphorylation. HEK 293T cells were transiently transfected with theindicated constructs. Twenty-four hours after transfection, cells wereserum starved and lysed. Shown are immunoblots of immunoprecipitatedERBB4 probed with the indicated antibodies. Lysates were immunoprobedwith an anti α-tubulin antibody. (FIG. 1C and FIG. 1D) ERBB4 mutantsexhibit increased in vitro kinase activity. (FIG. 1C) HEK 293T cellswere transiently transfected as in (FIG. 1B). Twenty-four hours aftertransfection, cells were either grown in 10% serum or serum starved andthen lysed. Protein lysates were immunoprecipitated and used in a kinaseassay. (FIG. 1D) The same samples that were used in the kinase assaywere immunoblotted with ERBB4 antibody and lysates were blotted withα-tubulin (ns=nonspecific; KD=kinase dead). (FIG. 1E) ERBB4 mutantsexhibit increased in vitro kinase activity. HEK 293T cells weretransiently transfected as in (FIG. 1B). Equivalent amounts of proteinfrom cell lysates were immunoprecipitated and used in a kinase assay tomeasure receptor auto-phosphorylation. The same samples that were usedin the kinase assay were immunoblotted with ERBB4 antibody and lysateswere blotted with α-tubulin. KD=kinase dead. (FIG. 1F) Increased basalactivation of endogenous mutant ERBB4. Melanoma lines that harbor eitherWT or mutant ERBB4 were serum starved and then lysed, immunoprecipitatedfor ERBB4, then immunoblotted with α-PY20 or α-ERBB4. (FIG. 1G) MutantERBB4 has increased basal activity. Melanoma lines harboring either WTor mutant ERBB4 were serum deprived, lysed, immunoprecipitated forERBB4, and analyzed by immunoblotting with α-P-ERBB4 (P—Y1162) orα-ERBB4.

FIGS. 2A-2B: Mutant ERBB4 induces transformation and anchorageindependent growth in NIH 3T3 and SK-MeI-2 cells. (FIG. 2A) NIH 3T3cells were transfected with the indicated ERBB4 mutant or controlconstructs. The graph indicates the average number of transformed fociafter 10 days. (FIG. 2B) Growth in soft agar of melanoma SK-MeI-2 cellsstably expressing either vector, WT ERBB4 or various ERBB4 missensemutants. The graph indicates the number of colonies after 14 days.

FIGS. 3A-3G: Expression of mutant ERBB4 provides an essential cellsurvival signal in melanoma. (FIG. 3A) HEK 293 cells were transientlyco-transfected with either vector or WT ERBB4 together with eithercontrol vector or shRNAs that target ERBB4. Cell lysates were analyzedby immunoblotting using α-ERBB4. For normalization, lysates wereanalyzed in parallel by α-tubulin immunoblotting. (FIG. 3B) Cellstransduced with shRNA targeting ERBB4 were lysed and immunoprecipitatedusing α-ERBB4 beads. Immunoprecipitates were blotted with specificantibodies, as indicated. (FIGS. 3C-3G) shRNA-mediated ERBB4 knockdownin melanoma lines containing ERBB4 mutations results in reduced cellgrowth. Cells were seeded in 96-well plates and incubated for 13-17days. Plates were analyzed every other day for cell proliferation, wherethe average cell number at each time point was measured by determiningDNA content using SYBR Green I. Melanoma cells harboring ERBB4 mutationsstably transduced with shRNA constructs targeting ERBB4, but not thosestably transduced with the control vector only, showed decreased growthrelative to control. This did not occur in melanoma cells harboring WTERBB4.

FIGS. 4A-4B: Detection of mutations in ERBB4. Shown are eight matchedsets of two chromatograms each, illustrating somatic mutations in theERBB4 gene. In each case, the top sequence chromatogram was obtainedfrom normal tissue and the lower sequence chromatogram from theindicated tumors. Arrows indicate the location of missense mutations.The nucleotide and amino acid alterations are indicated below the tumorchromatograms; numbering of the mutation locations is based on SEQ IDNO: 1 (nucleotide) and SEQ ID NO: 2 (amino acid).

FIG. 5: Distribution of mutations in ERBB4, FL T1, EphB2, EphB6, PTK2B,and TIE1. Shown is a schematic of the domain structure of select PTKs.Arrows indicate positions of nonsynonymous mutations and boxes representfunctional domains (Rcpt L, receptor L; GFR, growth factor receptor;PTK, protein tyrosine kinase; IG, immunoglobin; IGc2, immunoglobin C-2Type; Eph Rcpt, ephrin receptor; FNIII, fibronectin type III; SAM,sterile alpha motif; FERM, protein 4.1, ezrin, radixin, moesin domain;Focal AT, focal adhesion targeting region).

FIGS. 6A-6B: Mutation spectra of single base pair substitutions. (FIG.6A) Shown is a Kinome mutation spectrum. The number of each of the sixclasses of base substitutions resulting in nonsynonymous changes in thekinome screen is shown. (FIG. 6B) Shown is a mutation spectrum of singlebase pair substitutions in ERBB4. The number of each of the six classesof base substitutions resulting in nonsynonymous changes in ERBB4 isshown.

FIG. 7: Specificity of phosphorylation site-specific antibodies. Shownis a series of immunoblots to detect phosphorylation status of ERBB4mutants. HEK 293T cells were transiently transfected with either vectoror ERBB4 E452K missense mutant. Cells were serum starved and then lysed.Shown are immunoblots of immunoprecipitated ERBB4 probed with severalanti-phosphoERBB4 (Y1162; Y1284), or total ERBB4 antibodies in thepresence or absence of phosphorylated (pPep) or unphosphorylated (Pep)competitive peptide.

FIG. 8: Increased basal activation of endogenous mutant ERBB4. Shown isa set of two immunoblots demonstrating detection of phosphorylated ERBB4in melanoma cell lines expressing WT or mutant ERBB4. MM lines thatharbor either WT or mutant ERBB4 cells were either grown in 10% serum orserum starved and then lysed. Shown are immunoblots ofimmunoprecipitated ERBB4 probed with the indicated antibodies.

FIGS. 9A-9C: Effect of ERBB4 mutations on cell growth in NIH 3T3 andSK-MeI-2 cells. (FIG. 9A) Growth in soft agar of NIH 3T3 cellsexpressing either vector, WT ERBB4 or various ERBB4 missense mutants.The graph indicates the number of colonies after 14 days. (FIG. 9B andFIG. 9C) Detection of ERBB4 protein expression in stable transfectantsof SK-MeI-2 melanoma cells by western blot analysis. Lysates from thedifferent clones stably transfected with an empty vector, human ERBB4 orthe indicated ERBB4 mutants were immunoprecipitated and immunoblottedwith ERBB4 antibody (FIG. 9B). Anchorage independent proliferation ofSK-MeI-2 cell clones expressing the indicated constructs was assessed bymeasuring colony growth in soft agar (FIG. 9C). The graph indicates thenumber of colonies observed after 14 days of growth.

FIGS. 10A-10G: Melanoma lines expressing ERBB4 mutants exhibit increasedsensitivity to ERBB inhibition by lapatinib. (FIG. 10A) Representativedose response curves showing lapatinib efficacy against ERBB4 mutantcell lines compared to WT ERBB4 cell lines. Cells were treated for 72hours in the presence of increasing concentrations (0.01-30 μM) oflapatinib, and relative cell number was estimated by methylene blueprotein staining and plotted as percent survival when compared tovehicle-treated control versus Log(lapatinib) nM (where 1 is 10 nMlapatinib). Fitted lines were generated using 4-parameter nonlinearregression via GraphPad Prism. (FIG. 10B) ERBB4 mutant cells lines haveincreased sensitivity to lapatinib compared to WT ERBB4 cell lines. TheIC₅₀ values for inhibition of cell growth by 72 hour treatment withlapatinib of a larger panel of lines harboring WT and mutant ERBB4 wereanalyzed using GraphPad Prism v.5 (n=3). (FIG. 10C) Immunoprecipitationand western blot analysis of ERBB4 autophosphorylation in cells treatedwith lapatinib. Cells were treated for 1 hour with lapatinib or vehiclealone as control. Lysates were immunoprecipitated with α-ERBB4 followedby western blot analysis with α-ERBB4 and α-P-ERBB4 (Y1162). (FIG. 10D)Melanoma lines expressing mutant ERBB4 exhibit increased lapatinibsensitivity with respect to ERBB4 and AKT phosphorylation. The activityof ERBB4, AKT and ERBB2 was determined by immunoblotting withphospho-specific antibodies. Cells were treated for 1 hour with 5 μMlapatinib or vehicle alone. Lysates were immunoprecipitated usingα-ERBB2 or α-ERBB4. Lysates and immunoprecipitates were analyzed bywestern blotting using the indicated antibodies. Shown arerepresentative blots. (FIG. 10E) Quantitative assessment of data from 2cell lines harboring WT ERBB4 and 3 cell lines harboring mutant ERBB4that were performed similarly to (FIG. 10D). The ratio of bandintensities of (P—Y1162)-ERBB4/ERBB4, (P)-5473-AKT/AKT and(P—Y1248)-ERBB2/ERBB2 for each cell line are shown. (FIG. 10F) MutantERBB4 cells have increased sub-G1 population in the presence oflapatinib compared to WT ERBB4 cells. Shown are representative plots ofFACS analysis of 31T (WT) and 12T (E563K) showing cell cycledistribution (PI staining, x-axis) versus cell counts (y-axis). (FIG.10G) Quantitation of FACS-sorted lapatinib-treated cells. The percentapoptotic cells were determined based on the sub-G1 population forvehicle-treated cells or lapatinib-treated cells.

FIG. 11: Effects of ERBB4 mutation on AKT and ERK phosphorylation.Melanoma cell lines containing either WT or mutant ERBB4 were harvestedand analyzed by immunoblot. Shown are immunoblots of lysates probed withthe indicated antibodies (α-P-ERK1/2—recognizes phosphorylation of T202and Y204 on ERK1, and T185 and Y187 on ERK2).

FIG. 12: Knockdown of ERBB4 protein causes reduced activation of the AKTpathway but not of the ERK pathway. Melanoma cells lines containingeither WT or mutant ERBB4 were harvested and analyzed by western blot.Shown are immunoblots of lysates probed with the indicated antibodies.

FIGS. 13A-13B: Rescue of oncogene dependence by exogenous non-targetableERBB4. (FIG. 13A) Melanoma cells harboring mutant ERBB4 stablyexpressing control or ERBB4 shRNA #6 transduced with either vector ornon-targetable (NT) ERBB4 were analyzed by immunoblotting with theindicated antibodies. As a loading control, lysates were immunoblottedwith α-tubulin. (FIG. 13B) Melanoma cells expressing vector or the ERBB4shRNA #6 transduced with a vector or NT ERBB4 were evaluated for cellproliferation by measuring the average cell number at each time point bydetermining DNA content using SYBR Green I.

FIGS. 14A-14B: Effect of lapatinib in ERK1/2 signaling pathways. (FIG.14A) Melanoma lines expressing mutant ERBB4 exhibit increased lapatinibsensitivity with respect to ERK1 and ERK2 phosphorylation. Cells weretreated for 72 hours with 5 μM lapatinib or vehicle as control. Theactivity of ERK1 and ERK2 was determined by immunoblotting withphospho-specific antibodies. Total ERK protein was also determined byimmunoblotting. Shown are representative blots. (FIG. 14B) Quantitativeassessment of data from one melanoma cell line harboring mutant ERBB4.The ratio of band intensities of P-ERK1/ERK1 or P-ERK2/ERK2 was analyzedfor each melanoma cell line.

SEQUENCE LISTING

The nucleic and amino acid sequences listed in the accompanying sequencelisting are shown using standard letter abbreviations for nucleotidebases, and three letter code for amino acids, as defined in 37 C.F.R.1.822. Only one strand of each nucleic acid sequence is shown, but thecomplementary strand is understood as included by any reference to thedisplayed strand. The Sequence Listing is submitted as an ASCII textfile, created on Jan. 19, 2014, 46.4 KB, which is incorporated byreference herein. In the accompanying sequence listing:

SEQ ID NOs: 1 and 2 are the nucleotide and amino acid sequences,respectively, of human ERBB4 (GenBank Accession No. NM_(—)005235.2,deposited Jul. 28, 2006). Seven mutations identified in melanoma tumorsare indicated (G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614Ain the nucleotide sequence; E317K, E452K, E542K, R544W, E563K, E836K andE872K in the amino acid sequence).

SEQ ID NOs: 3-31 are the nucleotide sequences of forward primers used toPCR amplify the coding region of human ERBB4.

SEQ ID NOs: 32-60 are the nucleotide sequences of reverse primers usedto PCR amplify the coding region of human ERBB4.

SEQ ID NO: 61 is the nucleotide sequences of the primer used to sequencethe coding region of human ERBB4.

SEQ ID NOs: 62 and 63 are the nucleotide sequences of primers used toclone human ERBB4.

SEQ ID NOs: 64-70 are the nucleotide sequences of forward primers usedto PCR amplify the kinase domain of human ERBB4.

SEQ ID NOs: 71-77 are the nucleotide sequences of reverse primers usedto PCR amplify the kinase domain of human ERBB4.

SEQ ID NO: 78 is the nucleotide sequences of the forward primer used tosequence the kinase domain of human ERBB4.

SEQ ID NO: 79 is the nucleotide sequences of the reverse primer used tosequence the kinase domain of human ERBB4.

DETAILED DESCRIPTION I. Introduction

PTK signaling pathways can be deregulated by a variety of mechanisms inhuman tumors. Described herein is a comprehensive mutational analysis ofthe PTK family, which revealed numerous novel somatic mutations.Surprisingly, the analysis identified two PTK genes that had mutationsin over 10% of MM cases (FLT1 and PTK2B) and one gene that had mutationsin over 18% of MM cases (ERBB4, a member of the EGFR family). The highfrequency of mutations identified in ERBB4, their co-localization, andthe identification of two identical missense mutations in multiple MMcases, suggest that these mutations play a role in tumorigenesis.

To evaluate the effect of mutations in ERBB4, seven mutations thataffect residues that are conserved in EGFR, and are located at residuesnear EGFR mutations that have been described in other tumor types, werecloned and their kinase activity was examined. The results of thisanalysis showed that mutant ERBB4 has increased autophosphorylationactivity compared to wild type (WT) ERBB4. Expression of mutant ERBB4 inNIH 3T3 cells and human melanoma cells increased their growth on softagar and colony formation ability. Furthermore, immunoblots of melanomacells harboring ERBB4 mutations exhibited increased activity of thePI3K/AKT pathway, as evidenced by an increase in phosphorylated AKT.These functional assays indicated that the ERBB4 mutations identifiedherein promote cellular phenotypes typical of neoplastic cells, such asincreased transformation ability and anchorage-independent growth.

The combination of genetic, biochemical and cellular data disclosedherein indicates that ERBB4 functions as an oncogene in MM. This findingis consistent with previously reported alterations of members of theEGFR family, which have been shown to be mutated as well as amplified(Sharma et al., Nat. Rev. Cancer 7:169-181, 2007). In addition, ERBB4has previously been shown to be involved in enhanced proliferation ofbreast cancer cells (Junttila et al., Cancer Res. 65(4):1384-1393, 2005)and non-small cell lung cancer cells (Starr et al., Int. J. Cancer119:269-274, 2006). Importantly, cells containing mutations in ERBB4were associated with enhanced and selective sensitivity to anFDA-approved ERBB4 inhibitor compared to WT cells. These results suggestthat patients with melanoma containing one or more ERBB4 mutations maybenefit from therapy directed at mutant ERBB4.

II. Abbreviations

-   -   ARAF v-raf murine sarcoma 3611 viral oncogene homolog    -   BRAF B-Raf proto-oncogene serine/threonine-protein kinase    -   CRAF v-raf-1 murine leukemia viral oncogene homolog 1    -   DMEM Dulbecco's modified eagle medium    -   DMSO Dimethyl sulfoxide    -   DNA Deoxyribonucleic acid    -   EGFR Epidermal growth factor receptor    -   ELISA Enzyme-linked immunosorbent assay    -   FBS Fetal bovine serum    -   GFR Growth factor receptor    -   HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog    -   IC₅₀ Inhibitory concentration 50    -   IG Immunoglobulin    -   KD Kinase dead    -   KO Knockout    -   KRAS v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog    -   MM Metastatic melanoma    -   NRAS Neuroblastoma RAS viral oncogene homolog    -   NT Non-targetable    -   PAGE Polyacrylamide-gel electrophoresis    -   PBS Phosphate buffered saline    -   PCR Polymerase chain reaction    -   PI3K Phosphoinositide 3-kinase    -   RNA Ribonucleic acid    -   RNAi RNA interference    -   RT Reverse transcriptase    -   SAM Sterile alpha motif    -   SDS Sodium dodecyl sulfate    -   shRNA Short hairpin RNA    -   siRNA Small interfering RNA    -   SNP Single nucleotide polymorphism    -   TKI Tyrosine kinase inhibitor    -   WT Wild type

III. Terms

Unless otherwise noted, technical terms are used according toconventional usage. Definitions of common terms in molecular biology maybe found in Benjamin Lewin, Genes V, published by Oxford UniversityPress, 1994 (ISBN 0-19-854287-9); Kendrew et al. (eds.), TheEncyclopedia of Molecular Biology, published by Blackwell Science Ltd.,1994 (ISBN 0-632-02182-9); and Robert A. Meyers (ed.), Molecular Biologyand Biotechnology: a Comprehensive Desk Reference, published by VCHPublishers, Inc., 1995 (ISBN 1-56081-569-8).

In order to facilitate review of the various embodiments of thedisclosure, the following explanations of specific terms are provided:

AKT: As used herein, the term “AKT” includes AKT1, AKT2 and AKT3. TheAKT1 gene encodes a serine-threonine protein kinase that iscatalytically inactive in serum-starved primary and immortalizedfibroblasts. AKT1 and the related AKT2 are activated by platelet-derivedgrowth factor. The activation, which occurs through phosphatidylinositol3-kinase, is rapid and specific, and it is abrogated by mutations in thepleckstrin homology domain of AKT1. AKT1 is also known as v-akt murinethymoma viral oncogene homolog 1, PKB; RAC; PRKBA; MGC99656; PKB-ALPHA;and RAC-ALPHA. The AKT2 gene is a putative oncogene encoding a proteinbelonging to a subfamily of serine/threonine kinases containing SH2-like(Src homology 2-like) domains. The Akt2 protein is a general proteinkinase capable of phosphorylating several known proteins. AKT2 is alsoknown as v-akt murine thymoma viral oncogene homolog 2; PKBB; PRKBB;PKBBETA; and RAC-BETA. AKT3 is a member of the AKT (also called PKB)serine/threonine protein kinase family. AKT kinases are known to beregulators of cell signaling in response to insulin and growth factors.They are involved in a wide variety of biological processes includingcell proliferation, differentiation, apoptosis, tumorigenesis, as wellas glycogen synthesis and glucose uptake. The Akt3 protein kinase hasbeen shown to be stimulated by platelet-derived growth factor (PDGF),insulin, and insulin-like growth factor 1 (IGF1). AKT3 is also known asv-akt murine thymoma viral oncogene homolog 3; protein kinase B, gamma;PKBG; PRKBG; STK-2; PKB-GAMMA; RAC-gamma; RAC-PK-gamma; andDKFZp434N0250. Members of the AKT protein family are also called proteinkinases B (PKB) in the literature.

Antibody: A polypeptide ligand comprising at least a light chain orheavy chain immunoglobulin variable region which specifically recognizesand binds an epitope of an antigen. Antibodies are composed of a heavyand a light chain, each of which has a variable region, termed thevariable heavy (V_(H)) region and the variable light (V_(L)) region.Together, the V_(H) region and the V_(L) region are responsible forbinding the antigen recognized by the antibody.

Antibodies include intact immunoglobulins and the variants and portionsof antibodies well known in the art, such as Fab fragments, Fab′fragments, F(ab)′₂ fragments, single chain Fv proteins (“scFv”), anddisulfide stabilized Fv proteins (“dsFv”). A scFv protein is a fusionprotein in which a light chain variable region of an immunoglobulin anda heavy chain variable region of an immunoglobulin are bound by alinker, while in dsFvs, the chains have been mutated to introduce adisulfide bond to stabilize the association of the chains. The term alsoincludes genetically engineered forms such as chimeric antibodies (forexample, humanized murine antibodies), heteroconjugate antibodies (suchas, bispecific antibodies). See also, Pierce Catalog and Handbook,1994-1995 (Pierce Chemical Co., Rockford, Ill.); Kuby, J., Immunology,3^(rd) Ed., W.H. Freeman & Co., New York, 1997.

Typically, a naturally occurring immunoglobulin has heavy (H) chains andlight (L) chains interconnected by disulfide bonds. There are two typesof light chain, lambda (λ) and kappa (k). There are five main heavychain classes (or isotypes) which determine the functional activity ofan antibody molecule: IgM, IgD, IgG, IgA and IgE.

Each heavy and light chain contains a constant region and a variableregion, (the regions are also known as “domains”). In combination, theheavy and the light chain variable regions specifically bind theantigen. Light and heavy chain variable regions contain a “framework”region interrupted by three hypervariable regions, also called“complementarity-determining regions” or “CDRs.” The extent of theframework region and CDRs have been defined (see, Kabat et al.,Sequences of Proteins of Immunological Interest, U.S. Department ofHealth and Human Services, 1991, which is hereby incorporated byreference). The Kabat database is now maintained online. The sequencesof the framework regions of different light or heavy chains arerelatively conserved within a species, such as humans. The frameworkregion of an antibody, that is the combined framework regions of theconstituent light and heavy chains, serves to position and align theCDRs in three-dimensional space.

The CDRs are primarily responsible for binding to an epitope of anantigen. The CDRs of each chain are typically referred to as CDR1, CDR2,and CDR3, numbered sequentially starting from the N-terminus, and arealso typically identified by the chain in which the particular CDR islocated. Thus, a V_(H) CDR3 is located in the variable domain of theheavy chain of the antibody in which it is found, whereas a V_(L) CDR1is the CDR1 from the variable domain of the light chain of the antibodyin which it is found. Antibodies with different specificities (i.e.different combining sites for different antigens) have different CDRs.Although it is the CDRs that vary from antibody to antibody, only alimited number of amino acid positions within the CDRs are directlyinvolved in antigen binding. These positions within the CDRs are calledspecificity determining residues (SDRs).

References to “V_(H)” or “VH” refer to the variable region of animmunoglobulin heavy chain, including that of an Fv, scFv, dsFv or Fab.References to “V_(L)” or “VL” refer to the variable region of animmunoglobulin light chain, including that of an Fv, scFv, dsFv or Fab.

A “monoclonal antibody” is an antibody produced by a single clone of Blymphocytes or by a cell into which the light and heavy chain genes of asingle antibody have been transfected. Monoclonal antibodies areproduced by methods known to those of skill in the art, for instance bymaking hybrid antibody-forming cells from a fusion of myeloma cells withimmune spleen cells. Monoclonal antibodies include humanized monoclonalantibodies.

A “chimeric antibody” has framework residues from one species, such ashuman, and CDRs (which generally confer antigen binding) from anotherspecies, such as a murine antibody that specifically binds a targetantigen.

A “humanized” immunoglobulin is an immunoglobulin including a humanframework region and one or more CDRs from a non-human (for example amouse, rat, or synthetic) immunoglobulin. The non-human immunoglobulinproviding the CDRs is termed a “donor,” and the human immunoglobulinproviding the framework is termed an “acceptor.” In one embodiment, allthe CDRs are from the donor immunoglobulin in a humanizedimmunoglobulin. Constant regions need not be present, but if they are,they must be substantially identical to human immunoglobulin constantregions, i.e., at least about 85-90%, such as about 95% or moreidentical. Hence, all parts of a humanized immunoglobulin, exceptpossibly the CDRs, are substantially identical to corresponding parts ofnatural human immunoglobulin sequences. A “humanized antibody” is anantibody comprising a humanized light chain and a humanized heavy chainimmunoglobulin. A humanized antibody binds to the same antigen as thedonor antibody that provides the CDRs. The acceptor framework of ahumanized immunoglobulin or antibody may have a limited number ofsubstitutions by amino acids taken from the donor framework. Humanizedor other monoclonal antibodies can have additional conservative aminoacid substitutions which have substantially no effect on antigen bindingor other immunoglobulin functions. Humanized immunoglobulins can beconstructed by means of genetic engineering (see for example, U.S. Pat.No. 5,585,089).

A “human” antibody (also called a “fully human” antibody) is an antibodythat includes human framework regions and all of the CDRs from a humanimmunoglobulin. In one example, the framework and the CDRs are from thesame originating human heavy and/or light chain amino acid sequence.However, frameworks from one human antibody can be engineered to includeCDRs from a different human antibody. All parts of a humanimmunoglobulin are substantially identical to corresponding parts ofnatural human immunoglobulin sequences.

Antisense compound: Refers to an oligomeric compound that is at leastpartially complementary to the region of a target nucleic acid molecule(such as a miR gene product) to which it hybridizes. As used herein, anantisense compound that is “specific for” a target nucleic acid moleculeis one which specifically hybridizes with and modulates expression ofthe target nucleic acid molecule. As used herein, a “target” nucleicacid is a nucleic acid molecule to which an antisense compound isdesigned to specifically hybridize and modulate expression.

Nonlimiting examples of antisense compounds include primers, probes,antisense oligonucleotides, siRNAs, miRNAs, shRNAs and ribozymes. Assuch, these compounds can be introduced as single-stranded,double-stranded, circular, branched or hairpin compounds and can containstructural elements such as internal or terminal bulges or loops.Double-stranded antisense compounds can be two strands hybridized toform double-stranded compounds or a single strand with sufficientself-complementarity to allow for hybridization and formation of a fullyor partially double-stranded compound. In particular examples herein,the antisense compound is an antisense oligonucleotide, siRNA orribozyme.

Antisense oligonucleotide: As used herein, an “antisenseoligonucleotide” is a single-stranded antisense compound that is anucleic acid-based oligomer. An antisense oligonucleotide can includeone or more chemical modifications to the sugar, base, and/orinternucleoside linkages. Generally, antisense oligonucleotides are“DNA-like” such that when the antisense oligonucleotide hybridizes to atarget RNA molecule, the duplex is recognized by RNase H (an enzyme thatrecognizes DNA:RNA duplexes), resulting in cleavage of the RNA.

Array: An arrangement of molecules, such as biological macromolecules(such as peptides or nucleic acid molecules) or biological samples (suchas tissue sections), in addressable locations on or in a substrate. A“microarray” is an array that is miniaturized so as to require or beaided by microscopic examination for evaluation or analysis. Arrays aresometimes called DNA chips or biochips.

The array of molecules (“features”) makes it possible to carry out avery large number of analyses on a sample at one time. In certainexample arrays, one or more molecules (such as an oligonucleotide probe)will occur on the array a plurality of times (such as twice), forinstance to provide internal controls. The number of addressablelocations on the array can vary, for example from at least two, at leastfour, at least six, to at least 9, at least 10, at least 14, at least15, at least 20, at least 30, at least 50, at least 75, at least 100, atleast 150, at least 200, at least 300, at least 500, least 550, at least600, at least 800, at least 1000, or more. In a particular example, anarray includes 2-100 addressable locations, such as 4-20 addressablelocations. In particular examples, an array consists essentially ofoligonucleotide probes specific for ERBB4 nucleic acid moleculescomprising mutations selected from G949A, G1354A, G1624A, C1630T,G1687A, G2506A and G2614A (numbered with reference to SEQ ID NO: 1).

In particular examples, an array includes nucleic acid molecules, suchas oligonucleotide sequences that are at least 15 nucleotides in length,such as about 15-40 nucleotides in length.

Within an array, each arrayed sample is addressable, in that itslocation can be reliably and consistently determined within at least twodimensions of the array. The feature application location on an arraycan assume different shapes. For example, the array can be regular (suchas arranged in uniform rows and columns) or irregular. Thus, in orderedarrays the location of each sample is assigned to the sample at the timewhen it is applied to the array, and a key may be provided in order tocorrelate each location with the appropriate target or feature position.Often, ordered arrays are arranged in a symmetrical grid pattern, butsamples could be arranged in other patterns (such as in radiallydistributed lines, spiral lines, or ordered clusters). Addressablearrays usually are computer readable, in that a computer can beprogrammed to correlate a particular address on the array withinformation about the sample at that position (such as hybridization orbinding data, including for instance signal intensity). In some examplesof computer readable formats, the individual features in the array arearranged regularly, for instance in a Cartesian grid pattern, which canbe correlated to address information by a computer.

Candidate: As used herein, a “candidate” for treatment with an ERBB4inhibitor is a melanoma patient that is likely to respond favorably totreatment with the ERBB4 inhibitor. Candidates for ERBB4 inhibitortherapy are melanoma patients that have a mutation in the ERBB4 genethat results in an increase in ERBB4 expression, or results inexpression of an ERBB4 protein with increased kinase activity. In someembodiments, the candidate is a melanoma patient with an ERBB4 genecomprising a mutation selected from G949A, G1354A, G1624A, C1630T,G1687A, G2506A and G2614A (numbered with reference to SEQ ID NO: 1). Insome embodiment, the ERBB4 protein comprises a mutation selected fromE317K, E452K, E542K, R544W, E563K, E836K and E872K (numbered withreference to SEQ ID NO: 2).

Clinical outcome: Refers to the health status of a patient followingtreatment for a disease or disorder, or in the absence of treatment.Clinical outcomes include, but are not limited to, an increase in thelength of time until death, a decrease in the length of time untildeath, an increase in the chance of survival, an increase in the risk ofdeath, survival, disease-free survival, chronic disease, metastasis,advanced or aggressive disease, disease recurrence, death, and favorableor poor response to therapy.

Decrease in survival: As used herein, “decrease in survival” refers to adecrease in the length of time before death of a patient, or an increasein the risk of death for the patient. A decrease in survival also canrefer to a decrease in the average time to death in a group, such as agroup of patients diagnosed with melanoma.

Epidermal growth factor receptor (EGFR) family: A family of proteintyrosine kinases (PTKs), also known as the ERBB family. The ERBB PTKfamily includes four receptor kinases, ERBB1 (EGFR1, HER1), ERBB2(c-Neu, HER2), ERBB3 (HER3) and ERBB4 (HER4). The ERBB kinases regulatea wide range of cellular responses, including cell proliferation,survival, migration and differentiation. ERBB signaling pathways areknown to be altered in a wide variety of cancers.

ERBB4: A member of the EGFR family that encodes a protein ofapproximately 180 kD. ERBB4 encodes a single-pass type I membraneprotein with multiple cysteine rich domains, a transmembrane domain, atyrosine kinase domain, a phosphotidylinositol-3 kinase binding site anda PDZ domain binding motif. ERBB4 is expressed as four alternativelyspliced isoforms. The protein binds to and is activated by neuregulinsand other factors and induces a variety of cellular responses, includingmitogenesis and differentiation. Multiple proteolytic events allow forthe release of a cytoplasmic fragment and an extracellular fragment.Mutations in ERBB4 have been associated with cancer.

ERBB4 inhibitor: An ERBB4 inhibitor refers to any compound that inhibitsexpression or activity of ERBB4, such as kinase activity of ERBB4.Inhibitor compounds include, but are not limited to, small molecules,polypeptides and nucleic acid molecules (such as antisense compounds).In some embodiments, an ERBB4 inhibitor is a broad-spectrum inhibitorthat inhibits activity of multiple members of the EGFR family. EGFRfamily inhibitors are known in the art (see, for example, PCTPublication Nos. WO 2008/005983, WO 03/012072 and WO 03/070912; and USPatent Application Publication Nos. 2006/0233808 and 2006/0128636). Insome embodiments, the ERBB4 inhibitor selectively inhibits expression oractivity of ERBB4, and not other EGFR family members (see, for example,U.S. Pat. No. 5,811,098). In some embodiments, the ERBB4 inhibitor is akinase inhibitor. Kinase inhibitors are well known in the art (see, forexample, US Patent Application Publication Nos. 2008/0031893;2006/0148824; and 2002/0156083). In particular examples, the ERBB4inhibitor is lapatinib (Burris et al., J. Clin. Oncol. 23(23):5305-5313,2005).

Genomic DNA: The DNA found within the nucleus and containing anorganism's genome, which is passed on to its offspring as informationfor continued replication and/or propagation and/or survival of theorganism. The term can be used to distinguish between other types ofDNA, such as DNA found within plasmids or organelles.

Inhibitor: As used herein, the term “inhibitor” includes any type ofmolecule that inhibits the expression or activity of a target gene orprotein. An inhibitor can be any type of compound, such as a smallmolecule, antibody or antisense compound.

Kinase: An enzyme that catalyzes the transfer of a phosphate, such asfrom ATP, to a substrate. As used herein, an increase or decrease in“kinase activity” of a protein (e.g. ERBB4) refers to an increase ordecrease in the ability of the protein to phosphorylate a substrate,such as a protein.

Label: An agent capable of detection, for example by ELISA,spectrophotometry, flow cytometry, or microscopy. For example, a labelcan be attached to a nucleic acid molecule or protein, therebypermitting detection of the nucleic acid molecule or protein. Examplesof labels include, but are not limited to, radioactive isotopes, enzymesubstrates, co-factors, ligands, chemiluminescent agents, fluorophores,haptens, enzymes, and combinations thereof. Methods for labeling andguidance in the choice of labels appropriate for various purposes arediscussed for example in Sambrook et al. (Molecular Cloning: ALaboratory Manual, Cold Spring Harbor, N.Y., 1989) and Ausubel et al.(In Current Protocols in Molecular Biology, John Wiley & Sons, New York,1998).

In some embodiments, the label is a fluorophore (“fluorescent label”).Fluorophores are chemical compounds, which when excited by exposure to aparticular wavelength of light, emits light (i.e., fluoresces), forexample at a different wavelength. Fluorophores can be described interms of their emission profile, or “color.” Green fluorophores, forexample Cy3, FITC, and Oregon Green, are characterized by their emissionat wavelengths generally in the range of 515-540%. Red fluorophores, forexample Texas Red, Cy5 and tetramethylrhodamine, are characterized bytheir emission at wavelengths generally in the range of 590-690%.

Examples of fluorophores that may be used are provided in U.S. Pat. No.5,866,366 to Nazarenko et al., and include for instance:4-acetamido-4′-isothiocyanatostilbene-2,2′ disulfonic acid, acridine andderivatives such as acridine and acridine isothiocyanate,5-(2′-aminoethyl)aminonaphthalene-1-sulfonic acid (EDANS),4-amino-N-[3-vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (LuciferYellow VS), N-(4-anilino-1-naphthyl)maleimide, anthranilamide, BrilliantYellow, coumarin and derivatives such as coumarin,7-amino-4-methylcoumarin (AMC, Coumarin 120),7-amino-4-trifluoromethylcouluarin (Coumaran 151); cyanosine;4′,6-diaminidino-2-phenylindole (DAPI);5′,5″-dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red);7-diethylamino-3-(4′-isothiocyanatophenyl)-4-methylcoumarin;diethylenetriamine pentaacetate;4,4′-diisothiocyanatodihydro-stilbene-2,2′-disulfonic acid;4,4′-diisothiocyanatostilbene-2,2′-disulfonic acid;5-[dimethylamino]naphthalene-1-sulfonyl chloride (DNS, dansyl chloride);4-(4′-dimethylaminophenylazo)benzoic acid (DABCYL);4-dimethylaminophenylazophenyl-4′-isothiocyanate (DABITC); eosin andderivatives such as eosin and eosin isothiocyanate; erythrosin andderivatives such as erythrosin B and erythrosin isothiocyanate;ethidium; fluorescein and derivatives such as 5-carboxyfluorescein(FAM), 5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF),2′7′-dimethoxy-4′5′-dichloro-6-carboxyfluorescein (JOE), fluorescein,fluorescein isothiocyanate (FITC), and QFITC(XRITC); fluorescamine;IR144; IR1446; Malachite Green isothiocyanate; 4-methylumbelliferone;ortho cresolphthalein; nitrotyrosine; pararosaniline; Phenol Red;B-phycoerythrin; o-phthaldialdehyde; pyrene and derivatives such aspyrene, pyrene butyrate and succinimidyl 1-pyrene butyrate; Reactive Red4 (Cibacron® Brilliant Red 3B-A); rhodamine and derivatives such as6-carboxy-X-rhodamine (ROX), 6-carboxyrhodamine (R6G), lissaminerhodamine B sulfonyl chloride, rhodamine (Rhod), rhodamine B, rhodamine123, rhodamine X isothiocyanate, sulforhodamine B, sulforhodamine 101and sulfonyl chloride derivative of sulforhodamine 101 (Texas Red);N,N,N′,N′-tetramethyl-6-carboxyrhodamine (TAMRA); tetramethyl rhodamine;tetramethyl rhodamine isothiocyanate (TRITC); riboflavin; rosolic acidand terbium chelate derivatives.

Other contemplated fluorophores include GFP (green fluorescent protein),Lissamine™, diethylaminocoumarin, fluorescein chlorotriazinyl,naphthofluorescein, 4,7-dichlororhodamine and xanthene and derivativesthereof. Other fluorophores known to those skilled in the art may alsobe used.

LY294002: A selective small molecule inhibitor of PI3K. LY294002 is alsoknown as 2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one (Vlahos etal., J Biol Chem 269:5241-5248, 1994). The molecular formula of LY294002is C₁₉H₁₇NO₃.

Melanoma: A form of cancer that originates in melanocytes (cells thatmake the pigment melanin). Melanocytes are found primarily in the skin,but are also present in the bowel and eye.

Metastasis: Refers to the spread of cancer cells from the original tumorto other sites in the body.

Mutation: Any change of the DNA sequence within a gene or chromosome. Insome instances, a mutation will alter a characteristic or trait(phenotype), but this is not always the case. Types of mutations includebase substitution point mutations (e.g., transitions or transversions),deletions, and insertions. Missense mutations are those that introduce adifferent amino acid into the sequence of the encoded protein; nonsensemutations are those that introduce a new stop codon. In the case ofinsertions or deletions, mutations can be in-frame (not changing theframe of the overall sequence) or frame shift mutations, which mayresult in the misreading of a large number of codons (and often leads toabnormal termination of the encoded product due to the presence of astop codon in the alternative frame).

This term specifically encompasses variations that arise through somaticmutation, for instance those that are found only in disease cells, butnot constitutionally, in a given individual. Examples of suchsomatically-acquired variations include the point mutations thatfrequently result in altered function of various genes that are involvedin development of cancers. This term also encompasses DNA alterationsthat are present constitutionally, that alter the function of theencoded protein in a readily demonstrable manner, and that can beinherited by the children of an affected individual. In this respect,the term overlaps with “polymorphism,” as discussed below, but generallyrefers to the subset of constitutional alterations that have arisenwithin the past few generations in a kindred and that are not widelydisseminated in a population group.

In some embodiments, a mutation in ERBB4 refers to a nucleotidesubstitution in the ERBB4 gene or cDNA, or an amino acid substitution inthe ERBB4 protein.

Oligonucleotide: A linear polynucleotide sequence of up to about 100nucleotide bases in length.

Patient or subject: As used herein, the term “patient” includes humanand non-human animals. The preferred patient for treatment is a human.“Patient” and “subject” are used interchangeably herein.

Pharmaceutically acceptable vehicles: The pharmaceutically acceptablecarriers (vehicles) useful in this disclosure are conventional.Remington's Pharmaceutical Sciences, by E. W. Martin, Mack PublishingCo., Easton, Pa., 15th Edition (1975), describes compositions andformulations suitable for pharmaceutical delivery of one or moretherapeutic compounds, molecules or agents.

In general, the nature of the carrier will depend on the particular modeof administration being employed. For instance, parenteral formulationsusually comprise injectable fluids that include pharmaceutically andphysiologically acceptable fluids such as water, physiological saline,balanced salt solutions, aqueous dextrose, glycerol or the like as avehicle. For solid compositions (for example, powder, pill, tablet, orcapsule forms), conventional non-toxic solid carriers can include, forexample, pharmaceutical grades of mannitol, lactose, starch, ormagnesium stearate. In addition to biologically-neutral carriers,pharmaceutical compositions to be administered can contain minor amountsof non-toxic auxiliary substances, such as wetting or emulsifyingagents, preservatives, and pH buffering agents and the like, for examplesodium acetate or sorbitan monolaurate.

Phosphoinositide-3 kinase (PI3K): A family of related enzymes that arecapable of phosphorylating the 3 position hydroxyl group of the inositolring of phosphatidylinositol. PI3Ks are also known asphosphatidylinositol-3-kinases. Class I PI3K are heterodimeric moleculescomposed of a regulatory subunit and a catalytic subunit. Class II andClass III PI3K are differentiated from Class I by their structure andfunction. Class II PI3K are composed of one of three catalytic isoforms(C2α, C2β, and C2γ), but have no regulatory proteins. Class III PI3Kexist as a heterodimers of a catalytic subunit (Vps34) and a regulatory(p150) subunit. Genes encoding PIK3 subunits include, for example,PIK3C2A, PIK3C2B, PIK3C2G, PIK3C3, PIK3CA, PIK3CB, PIK3CG, PIK3CD,PIK3R1, PIK3R2, PIK3R3, PIK3R4, PIK3R4, PIK3R5 and PIK3R6.

PI3K/Akt pathway: A signaling pathway involved in a number of cellularprocesses, such as cell growth, proliferation, differentiation,motility, survival, intracellular trafficking, metabolism andangiogenesis.

PI3K/Akt pathway inhibitor: Any compound that inhibits expression oractivity of a member of the PI3K pathway, such as, but not limited toPI3K or AKT. For example, the inhibitor can be a small molecule,antibody, antisense compound or polypeptide. In some examples, theantibody is a chimeric antibody, a humanized antibody or a humanantibody. In some examples, the antisense compound is an antisenseoligonucleotide, siRNA or ribozyme. Antibodies, antisense compounds andother inhibitors specific for members of the PI3K/Akt pathway are knownin the art and are commercially available. Exemplary inhibitors of thePI3K/Akt pathway are described herein, but are not intended to belimiting. In some examples, the small molecule inhibitor of PI3K isLY294002 (also known as2-(4-morpholinyl)-8-phenyl-4H-1-benzopyran-4-one; molecular formulaC₁₉H₁₇NO₃) or wortmannin (molecular formula C₂₃H₂₄O₈). In some examples,the small molecule inhibitor of Akt is UCN-01 (also known as7-hydroxystaurosporine and8,12-epoxy-1H,8H-2,7b,12a-triazadibenzo[a,g]cyclonona[cde]trinden-1-one,2,3,9,10,11,12-hexahydro-3-hydroxy-9-methoxy-8-methyl-10-(methylamino)).UCN-01 is a synthetic derivative of staurosporine with antineoplasticactivity. Antisense compounds specific for members for the PI3K/Aktpathway have been previously described. For example, U.S. PatentApplication Publication Nos. 2005/02772682 and 2004/0077580 disclosesiRNAs and antisense oligonucleotides specific for PI3K. In addition,U.S. Patent Application Publication Nos. 2008/0161547, 2004/0265999 and2003/0148974 describe antisense oligonucleotide and siRNA compounds thattarget AKT. Antibodies specific for members of the PI3K/Akt pathway havebeen described in the art and are commercially available from a varietyof sources. For example, PI3K antibodies are disclosed in U.S. PatentApplication Publication No. 2008/0014598.

Polymorphism: Variant in a sequence of a gene, or any genomic sequence,usually carried from one generation to another in a population.Polymorphisms can be those variations (nucleotide sequence differences)that, while having a different nucleotide sequence, produce functionallyequivalent gene products, such as those variations generally foundbetween individuals, different ethnic groups, and geographic locations.The term polymorphism also encompasses variations that produce geneproducts with altered function, i.e., variants in the gene sequence thatlead to gene products that are not functionally equivalent. This termalso encompasses variations that produce no gene product, an inactivegene product, a truncated gene product, or increased or increasedactivity gene product.

Polymorphisms can be referred to, for instance, by the nucleotideposition at which the variation exists, by the change in amino acidsequence caused by the nucleotide variation, or by a change in someother characteristic of the nucleic acid molecule or protein that islinked to the variation (e.g., an alteration of a secondary structuresuch as a stem-loop, or an alteration of the binding affinity of thenucleic acid for associated molecules, such as polymerases, RNAses, achange in the availability of a site for cleavage by a restrictionendonuclease, either the formation of a new site, or lose of a site, andso forth).

Polypeptide: A polymer in which the monomers are amino acid residueswhich are joined together through amide bonds. When the amino acids arealpha-amino acids, either the L-optical isomer or the D-optical isomercan be used. The terms “polypeptide” or “protein” as used herein areintended to encompass any amino acid sequence and include modifiedsequences such as glycoproteins. The term “polypeptide” is specificallyintended to cover naturally occurring proteins, as well as those whichare recombinantly or synthetically produced.

The term “residue” or “amino acid residue” includes reference to anamino acid that is incorporated into a protein, polypeptide, or peptide.

Conservative amino acid substitutions are those substitutions that, whenmade, least interfere with the properties of the original protein, thatis, the structure and especially the function of the protein isconserved and not significantly changed by such substitutions. Examplesof conservative substitutions are shown in the following table:

Original Residue Conservative Substitutions Ala Ser Arg Lys Asn Gln, HisAsp Glu Cys Ser Gln Asn Glu Asp His Asn; Gln Ile Leu, Val Leu Ile; ValLys Arg; Gln; Glu Met Leu; Ile Phe Met; Leu; Tyr Ser Thr Thr Ser Trp TyrTyr Trp; Phe Val Ile; Leu

Conservative substitutions generally maintain (a) the structure of thepolypeptide backbone in the area of the substitution, for example, as asheet or helical conformation, (b) the charge or hydrophobicity of themolecule at the target site, or (c) the bulk of the side chain.

The substitutions which in general are expected to produce the greatestchanges in protein properties will be non-conservative, for instancechanges in which (a) a hydrophilic residue, for example, seryl orthreonyl, is substituted for (or by) a hydrophobic residue, for example,leucyl, isoleucyl, phenylalanyl, valyl or alanyl; (b) a cysteine orproline is substituted for (or by) any other residue; (c) a residuehaving an electropositive side chain, for example, lysyl, arginyl, orhistadyl, is substituted for (or by) an electronegative residue, forexample, glutamyl or aspartyl; or (d) a residue having a bulky sidechain, for example, phenylalanine, is substituted for (or by) one nothaving a side chain, for example, glycine.

Preventing, treating or ameliorating a disease: “Preventing” a disease(such as metastatic melanoma) refers to inhibiting the full developmentof a disease. “Treating” refers to a therapeutic intervention thatameliorates a sign or symptom of a disease or pathological conditionafter it has begun to develop. “Ameliorating” refers to the reduction inthe number or severity of signs or symptoms of a disease.

Probes and primers: A probe comprises an isolated nucleic acid capableof hybridizing to a target nucleic acid. A detectable label or reportermolecule can be attached to a probe or primer. Typical labels includeradioactive isotopes, enzyme substrates, co-factors, ligands,chemiluminescent or fluorescent agents, haptens, and enzymes. Methodsfor labeling and guidance in the choice of labels appropriate forvarious purposes are discussed, for example in Sambrook et al. (InMolecular Cloning: A Laboratory Manual, CSHL, New York, 1989) andAusubel et al. (In Current Protocols in Molecular Biology, John Wiley &Sons, New York, 1998). In some embodiments, an “oligonucleotide” is aprobe or primer.

In a particular example, a probe includes at least one fluorophore, suchas an acceptor fluorophore or donor fluorophore. For example, afluorophore can be attached at the 5′- or 3′-end of the probe. Inspecific examples, the fluorophore is attached to the base at the 5′-endof the probe, the base at its 3′-end, the phosphate group at its 5′-endor a modified base, such as a T internal to the probe.

Probes are generally at least 15 nucleotides in length, such as at least15, at least 16, at least 17, at least 18, at least 19, least 20, atleast 21, at least 22, at least 23, at least 24, at least 25, at least26, at least 27, at least 28, at least 29, at least 30, at least 31, atleast 32, at least 33, at least 34, at least 35, at least 36, at least37, at least 38, at least 39, at least 40, at least 41, at least 42, atleast 43, at least 44, at least 45, at least 46, at least 47, at least48, at least 49, at least 50 at least 51, at least 52, at least 53, atleast 54, at least 55, at least 56, at least 57, at least 58, at least59, at least 60, at least 61, at least 62, at least 63, at least 64, atleast 65, at least 66, at least 67, at least 68, at least 69, at least70, or more contiguous nucleotides complementary to the target nucleicacid molecule, such as 15-70 nucleotides, 15-60 nucleotides, 15-50nucleotides, 15-40 nucleotides, or 15-30 nucleotides.

Primers are short nucleic acid molecules, for instance DNAoligonucleotides 10 nucleotides or more in length, which can be annealedto a complementary target nucleic acid molecule by nucleic acidhybridization to form a hybrid between the primer and the target nucleicacid strand. A primer can be extended along the target nucleic acidmolecule by a polymerase enzyme. Therefore, primers can be used toamplify a target nucleic acid molecule.

The specificity of a primer increases with its length. Thus, forexample, a primer that includes 30 consecutive nucleotides will annealto a target sequence with a higher specificity than a correspondingprimer of only 15 nucleotides. Thus, to obtain greater specificity,probes and primers can be selected that include at least 15, 20, 25, 30,35, 40, 45, 50, 55, 60, 65, 70 or more consecutive nucleotides. Inparticular examples, a primer is at least 15 nucleotides in length, suchas at least 15 contiguous nucleotides complementary to a target nucleicacid molecule. Particular lengths of primers that can be used topractice the methods of the present disclosure include primers having atleast 15, at least 16, at least 17, at least 18, at least 19, at least20, at least 21, at least 22, at least 23, at least 24, at least 25, atleast 26, at least 27, at least 28, at least 29, at least 30, at least31, at least 32, at least 33, at least 34, at least 35, at least 36, atleast 37, at least 38, at least 39, at least 40, at least 45, at least50, at least 55, at least 60, at least 65, at least 70, or morecontiguous nucleotides complementary to the target nucleic acid moleculeto be amplified, such as a primer of 15-70 nucleotides, 15-60nucleotides, 15-50 nucleotides, 15-40 nucleotides or 15-30 nucleotides.

Primer pairs can be used for amplification of a nucleic acid sequence,for example, by PCR, real-time PCR, or other nucleic-acid amplificationmethods known in the art. An “upstream” or “forward” primer is a primer5′ to a reference point on a nucleic acid sequence. A “downstream” or“reverse” primer is a primer 3′ to a reference point on a nucleic acidsequence. In general, at least one forward and one reverse primer areincluded in an amplification reaction.

Nucleic acid probes and primers can be readily prepared based on thenucleic acid molecules provided herein. It is also appropriate togenerate probes and primers based on fragments or portions of thesedisclosed nucleic acid molecules, for instance regions that encompassthe identified polymorphisms of interest. PCR primer pairs can bederived from a known sequence by using computer programs intended forthat purpose such as Primer (Version 0.5, © 1991, Whitehead Institutefor Biomedical Research, Cambridge, Mass.) or PRIMER EXPRESS® Software(Applied Biosystems, AB, Foster City, Calif.).

Prognosis: The likelihood of the clinical outcome for a subjectafflicted with a specific disease or disorder. With regard to cancer,the prognosis is a representation of the likelihood (probability) thatthe subject will survive (such as for one, two, three, four or fiveyears) and/or the likelihood (probability) that the tumor willmetastasize. A “poor prognosis” indicates a greater than 50% chance thatthe subject will not survive to a specified time point (such as one,two, three, four or five years), and/or a greater than 50% chance thatthe tumor will metastasize. In several examples, a poor prognosisindicates that there is a greater than 60%, 70%, 80%, or 90% chance thatthe subject will not survive and/or a greater than 60%, 70%, 80% or 90%chance that the tumor will metastasize. Conversely, a “good prognosis”indicates a greater than 50% chance that the subject will survive to aspecified time point (such as one, two, three, for or five years),and/or a greater than 50% chance that the tumor will not metastasize. Inseveral examples, a good prognosis indicates that there is a greaterthan 60%, 70%, 80%, or 90% chance that the subject will survive and/or agreater than 60%, 70%, 80% or 90% chance that the tumor will notmetastasize.

Protein tyrosine kinase (PTK): A family of proteins that catalyzephosphorylation of tyrosine residues in target proteins. PTKs playimportant roles in cellular signaling.

Ribozyme: A catalytic RNA molecule. In some cases, ribozymes can bind tospecific sites on other RNA molecules and catalyze the hydrolysis ofphosphodiester bonds in the RNA molecules.

RNA interference (RNAi): Refers to a cellular process that inhibitsexpression of genes, including cellular and viral genes. RNAi is a formof antisense-mediated gene silencing involving the introduction ofdouble stranded RNA-like oligonucleotides leading to thesequence-specific reduction of RNA transcripts. Double-stranded RNAmolecules that inhibit gene expression through the RNAi pathway includesiRNAs, miRNAs, and shRNAs.

Sample: A biological specimen containing genomic DNA, RNA, protein, orcombinations thereof, obtained from a subject. Examples include, but arenot limited to, peripheral blood, urine, saliva, tissue biopsy (such asskin tissue), surgical specimen, and autopsy material. In one example, asample includes a biopsy of a melanoma tumor or a sample of normaltissue (from a subject not afflicted with a known disease or disorder,such as a cancer-free subject).

Screening: As used herein, “screening” refers to the process used toevaluate and identify candidate agents that decrease kinase activity ofERBB4 protein. In some cases, screening involves contacting a candidateagent (such as a small molecule, peptide or nucleic acid molecule) withcells expressing ERBB4 and testing the effect of the agent on kinaseactivity of ERBB4. In some embodiments, the cells express WT ERBB4. Inother embodiments, the cells express mutant ERBB4, such as an ERBB4protein comprising a mutation selected from E317K, E452K, E542K, R544W,E563K, E836K and E872K (numbered with reference to SEQ ID NO: 2).

Short hairpin RNA (shRNA): A sequence of RNA that makes a tight hairpinturn and can be used to silence gene expression via the RNAi pathway.The shRNA hairpin structure is cleaved by the cellular machinery intosiRNA.

Small interfering RNA (siRNA): A double-stranded nucleic acid moleculethat modulates gene expression through the RNAi pathway. siRNA moleculesare generally 20-25 nucleotides in length with 2-nucleotide overhangs oneach 3′ end. However, siRNAs can also be blunt ended. Generally, onestrand of a siRNA molecule is at least partially complementary to atarget nucleic acid, such as a target mRNA. siRNAs are also referred toas “small inhibitory RNAs.”

Small molecule: A molecule, typically with a molecular weight less thanabout 1000 Daltons, or in some embodiments, less than about 500 Daltons,wherein the molecule is capable of modulating, to some measurableextent, an activity of a target molecule.

Specific hybridization: Specific hybridization refers to the binding,duplexing, or hybridizing of a molecule only or substantially only to aparticular nucleotide sequence when that sequence is present in acomplex mixture (e.g. total cellular DNA or RNA). Specific hybridizationmay also occur under conditions of varying stringency.

Hybridization conditions resulting in particular degrees of stringencywill vary depending upon the nature of the hybridization method ofchoice and the composition and length of the hybridizing DNA used.Generally, the temperature of hybridization and the ionic strength(especially the Na⁺ concentration) of the hybridization buffer willdetermine the stringency of hybridization. Calculations regardinghybridization conditions required for attaining particular degrees ofstringency are discussed by Sambrook et al. (In: Molecular Cloning: ALaboratory Manual, Cold Spring Harbor, N.Y., 1989 ch. 9 and 11). By wayof illustration only, a hybridization experiment may be performed byhybridization of a DNA molecule to a target DNA molecule which has beenelectrophoresed in an agarose gel and transferred to a nitrocellulosemembrane by Southern blotting (Southern, J. Mol. Biol. 98:503, 1975), atechnique well known in the art and described in Sambrook et al.(Molecular Cloning: A Laboratory Manual, Cold Spring Harbor, N.Y.,1989).

Traditional hybridization with a target nucleic acid molecule labeledwith [³²P]-dCTP is generally carried out in a solution of high ionicstrength such as 6×SSC at a temperature that is 20-25° C. below themelting temperature, T_(m), described below. For Southern hybridizationexperiments where the target DNA molecule on the Southern blot contains10 ng of DNA or more, hybridization is typically carried out for 6-8hours using 1-2 ng/ml radiolabeled probe (of specific activity equal to10⁹ CPM/μg or greater). Following hybridization, the nitrocellulosefilter is washed to remove background hybridization. The washingconditions should be as stringent as possible to remove backgroundhybridization but to retain a specific hybridization signal.

The term T_(m) represents the temperature (under defined ionic strength,pH and nucleic acid concentration) at which 50% of the probescomplementary to the target sequence hybridize to the target sequence atequilibrium. Because the target sequences are generally present inexcess, at T_(m) 50% of the probes are occupied at equilibrium. TheT_(m) of such a hybrid molecule may be estimated from the followingequation (Bolton and McCarthy, Proc. Natl. Acad. Sci. USA 48:1390,1962):

T _(m)=81.5° C.−16.6(log₁₀[Na⁺])+0.41(% G+C)−0.63(% formamide)−(600/l)

where l=the length of the hybrid in base pairs.

This equation is valid for concentrations of Na⁺ in the range of 0.01 Mto 0.4 M, and it is less accurate for calculations of Tm in solutions ofhigher [Na⁺]. The equation is also primarily valid for DNAs whose G+Ccontent is in the range of 30% to 75%, and it applies to hybrids greaterthan 100 nucleotides in length (the behavior of oligonucleotide probesis described in detail in Ch. 11 of Sambrook et al. (Molecular Cloning:A Laboratory Manual, Cold Spring Harbor, N.Y., 1989).

Thus, by way of example, for a 150 base pair DNA probe derived from acDNA (with a hypothetical % GC of 45%), a calculation of hybridizationconditions required to give particular stringencies may be made asfollows: For this example, it is assumed that the filter will be washedin 0.3×SSC solution following hybridization, thereby: [Na^(+]=)0.045 M;% GC=45%; Formamide concentration=0; l=150 base pairs;T_(m)=81.5−16.6(log₁₀[Na⁺])+(0.41×45)−(600/150); and so T_(m)=74.4° C.

The T_(m) of double-stranded DNA decreases by 1-1.5° C. with every 1%decrease in homology (Bonner et al., J. Mol. Biol. 81:123, 1973).Therefore, for this given example, washing the filter in 0.3×SSC at59.4-64.4° C. will produce a stringency of hybridization equivalent to90%; that is, DNA molecules with more than 10% sequence variationrelative to the target cDNA will not hybridize. Alternatively, washingthe hybridized filter in 0.3×SSC at a temperature of 65.4-68.4° C. willyield a hybridization stringency of 94%; that is, DNA molecules withmore than 6% sequence variation relative to the target cDNA moleculewill not hybridize. The above example is given entirely by way oftheoretical illustration. It will be appreciated that otherhybridization techniques may be utilized and that variations inexperimental conditions will necessitate alternative calculations forstringency.

Stringent conditions may be defined as those under which DNA moleculeswith more than 25%, 15%, 10%, 6% or 2% sequence variation (also termed“mismatch”) will not hybridize. Stringent conditions are sequencedependent and are different in different circumstances. Longer sequenceshybridize specifically at higher temperatures. Generally, stringentconditions are selected to be about 5° C. lower than the thermal meltingpoint T_(m) for the specific sequence at a defined ionic strength andpH. An example of stringent conditions is a salt concentration of atleast about 0.01 to 1.0 M Na ion concentration (or other salts) at pH7.0 to 8.3 and a temperature of at least about 30° C. for short probes(e.g. 10 to 50 nucleotides). Stringent conditions can also be achievedwith the addition of destabilizing agents such as formamide. Forexample, conditions of 5×SSPE (750 mM NaCl, 50 mM Na Phosphate, 5 mMEDTA, pH 7.4) and a temperature of 25-30° C. are suitable forallele-specific probe hybridizations.

The following is an exemplary set of hybridization conditions and is notmeant to be limiting:

Very High Stringency (detects sequences that share at least 90%identity) Hybridization: 5x SSC at 65° C. for 16 hours Wash twice: 2xSSC at room temperature (RT) for 15 minutes each Wash twice: 0.5x SSC at65° C. for 20 minutes each

High Stringency (detects sequences that share 80% identity or greater)Hybridization: 5x-6x SSC at 65° C.-70° C. for 16-20 hours Wash twice: 2xSSC at RT for 5-20 minutes each Wash twice: 1x SSC at 55° C.-70° C. for30 minutes each

Low Stringency (detects sequences that share greater than 50% identity)Hybridization: 6x SSC at RT to 55° C. for 16-20 hours Wash at leasttwice: 2x-3x SSC at RT to 55° C. for 20-30 minutes each.

A perfectly matched probe has a sequence perfectly complementary to aparticular target sequence. The test probe is typically perfectlycomplementary to a portion (subsequence) of the target sequence. Theterm “mismatch probe” refers to probes whose sequence is deliberatelyselected not to be perfectly complementary to a particular targetsequence.

Therapeutic: A generic term that includes both diagnosis and treatment.

Therapeutic agent: A chemical compound, small molecule, or othercomposition, such as an antisense compound, antibody, peptide, nucleicacid molecule, protease inhibitor, hormone, chemokine or cytokine,capable of inducing a desired therapeutic or prophylactic effect whenproperly administered to a subject. For example, therapeutic agents formelanoma include agents that prevent or inhibit development ormetastasis of melanoma. As used herein, a “candidate agent” is acompound selected for screening to determine if it can function as atherapeutic agent for melanoma. In some embodiments, a “candidate agent”is an agent screened to determine if is capable of increasing kinaseactivity of ERBB4. “Incubating” includes a sufficient amount of time foran agent to interact with a cell or tissue. “Contacting” includesincubating an agent in solid or in liquid form with a cell or tissue.“Treating,” when used to refer to the treatment of a cell or tissue witha therapeutic agent, includes contacting or incubating an agent with thecell or tissue.

Transformation: Refers to the transition of a normal cell to a malignantcell.

Tumor, neoplasia, malignancy or cancer: A neoplasm is an abnormal growthof tissue or cells that results from excessive cell division. Neoplasticgrowth can produce a tumor. The amount of a tumor in an individual isthe “tumor burden” which can be measured as the number, volume, orweight of the tumor. A tumor that does not metastasize is referred to as“benign.” A tumor that invades the surrounding tissue and/or canmetastasize is referred to as “malignant.” A “non-cancerous tissue” is atissue from the same organ wherein the malignant neoplasm formed, butdoes not have the characteristic pathology of the neoplasm. Generally,noncancerous tissue appears histologically normal. A “normal tissue” istissue from an organ, wherein the organ is not affected by cancer oranother disease or disorder of that organ. A “cancer-free” subject hasnot been diagnosed with a cancer of that organ and does not havedetectable cancer.

UCN-01 (7-hydroxystaurosporine): A synthetic derivative of staurosporinewith antineoplastic activity. UCN-01 inhibits many phosphokinases,including AKT, calcium-dependent protein kinase C, and cyclin-dependentkinases. The chemical structure name of UCN-01 is8,12-epoxy-1H,8H-2,7b,12a-triazadibenzo[a,g]cyclonona[cde]trinden-1-one,2,3,9,10,11,12-hexahydro-3-hydroxy-9-methoxy-8-methyl-10-(methylamino).

Wortmannin: A furanosteroid metabolite of the fungi Penicilliumfuniculosum, Talaromyces (Penicillium) wortmannii, is a specific,covalent inhibitor of PI3K. The molecular formula of wortmannin isC₂₃H₂₄O₈.

Unless otherwise explained, all technical and scientific terms usedherein have the same meaning as commonly understood by one of ordinaryskill in the art to which this disclosure belongs. The singular terms“a,” “an,” and “the” include plural referents unless context clearlyindicates otherwise. Similarly, the word “or” is intended to include“and” unless the context clearly indicates otherwise. Hence “comprisingA or B” means including A, or B, or A and B. It is further to beunderstood that all base sizes or amino acid sizes, and all molecularweight or molecular mass values, given for nucleic acids or polypeptidesare approximate, and are provided for description. Although methods andmaterials similar or equivalent to those described herein can be used inthe practice or testing of the present disclosure, suitable methods andmaterials are described below. All publications, patent applications,patents, and other references mentioned herein are incorporated byreference in their entirety. In case of conflict, the presentspecification, including explanations of terms, will control. Inaddition, the materials, methods, and examples are illustrative only andnot intended to be limiting.

IV. Overview of Several Embodiments

It is disclosed herein that melanoma patients exhibit a number ofdifferent mutations in PTK family members (see Table 4). In particular,it is demonstrated that ERBB4 is highly mutated in metastatic melanoma.Described herein are novel ERBB4 mutations, which result in expressionof ERBB4 protein with increased kinase activity. In addition, cellsexpressing mutant ERBB4 exhibit transformation capacity. The ERBB4mutations disclosed herein also activate the PI3K/AKT pathway.

Provided herein is a method of predicting the prognosis of a subjectdiagnosed with melanoma, comprising detecting the presence or absence ofa mutation in the ERBB4 gene, wherein the presence of a mutation in theERBB4 gene predicts a poor prognosis. A poor prognosis refers to anynegative clinical outcome. For example, in some embodiments, a poorprognosis is an increase in the likelihood of death. In someembodiments, a poor prognosis is an increase in the likelihood ofmetastasis of the melanoma.

Further provided is a method of selecting a subject diagnosed withmelanoma as a candidate for treatment with an ERBB4 inhibitor, aPI3K/AKT pathway inhibitor, or both, comprising detecting the presenceor absence of a mutation in the ERBB4 gene, wherein the presence of amutation in the ERBB4 gene indicates that the subject is a candidate fortreatment with an ERBB4 inhibitor, a PI3K/AKT pathway inhibitor, orboth.

In particular examples, the ERBB4 mutation is selected from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1).

In some embodiments, the method further comprises administering to thesubject an ERBB4 inhibitor, a PI3K/AKT pathway inhibitor, or both. Insome examples, the ERBB4 inhibitor is lapatinib. Agents that decreaseexpression or activity of ERBB4 or a member of the PI3K/AKT pathway(such as, but not limited to, AKT or PI3K) are known in the art, some ofwhich are described herein.

In some embodiments of the methods, the ERBB4 mutation results in anincrease in kinase activity of the ERBB4 protein. In particularexamples, the ERBB4 mutation introduces an amino acid change selectedfrom E317K, E452K, E542K, R544W, E563K, E836K and E872K (numbered withreference to SEQ ID NO: 2).

Methods of detecting mutations in a gene are well known in the art.Detection of one or more mutations in the ERBB4 gene can be accomplishedusing any suitable technique, such as those described in detail in thesections below. For example, ERBB4-specific primers can be used toamplify ERBB4 nucleic acid from a biological sample (such as a tumortissue sample or blood sample). The amplified molecule can then besequenced and compared to a reference ERBB4 sequence (such as SEQ ID NO:1), or compared with ERBB4 from a control sample such as a non-canceroustissue sample, to detect a mutation in ERBB4. ERBB4 amplificationprimers and sequencing primers can be designed according to well knownmethods. Examples of ERBB4 primers are provided in Table 1 and Table 3(SEQ ID NOs: 3-60 and 64-77). Mutations in ERBB4 can also be detectedusing oligonucleotides that specifically hybridize with a particularmutation. Hybridization of such oligonucleotides can be detected bylabeling the oligonucleotide with a detectable marker, such as afluorescent marker, enzymatic marker or radioisotope.

For detection of ERBB4 mutations, nucleic acid (such as DNA or RNA) canbe isolated from a biological sample according to well known methods. Insome embodiments, the biological sample is tissue sample, such as atumor tissue sample. In other embodiments, the biological sample is afluid sample, such as blood. For example, nucleic acid can be isolatedfrom cells obtained from a blood sample. In some embodiments, thebiological sample is obtained from a patient diagnosed with melanoma. Insome embodiments, the biological sample is obtained from a controlsubject.

Also provided is a method of identifying a therapeutic agent for thetreatment of a subject diagnosed with melanoma, comprising screeningcandidate agents to select an agent that decreases activity (such askinase activity) of ERBB4, thereby identifying a therapeutic agent forthe treatment of a subject with melanoma. In particular examples, theERBB4 mutation is selected from G949A, G1354A, G1624A, C1630T, G1687A,G2506A and G2614A (numbered with reference to SEQ ID NO: 1).

In some embodiments, the candidate agent is a small molecule,polypeptide (such as an antibody) or nucleic acid molecule (such as anantisense compound, including antisense oligonucleotides, siRNAs orribozymes). In some examples, screening comprises contacting thecandidate agents with cells expressing ERBB4. In some embodiments, thecells express WT ERBB4. In other embodiments, the cells express ERBB4protein comprising a mutation selected from E317K, E452K, E542K, R544W,E563K, E836K and E872K (numbered with reference to SEQ ID NO: 2). Insome embodiments, the therapeutic agent increases kinase activity ofERBB4 at least 2-fold, at least 3-fold, at least 4-fold or at least5-fold relative to untreated cells.

Further provided is a method of identifying a therapeutic agent for thetreatment of a subject diagnosed with melanoma, comprising screeningcandidate agents to select an agent that decreases expression oractivity of a member of the PI3K/AKT pathway, thereby identifying atherapeutic agent for the treatment of a subject with melanoma. In somecases, the agent decreases activity of AKT, such as by reducingphosphorylation of AKT. In some embodiments, the candidate agent is asmall molecule, polypeptide (such as an antibody) or nucleic acidmolecule (such as an antisense compound, including antisenseoligonucleotides, siRNAs or ribozymes).

Further provided herein are oligonucleotides that specifically hybridizewith an ERBB4 nucleic acid molecule, wherein the ERBB4 nucleic acidmolecule comprises a mutation selected from G949A, G1354A, G1624A,C1630T, G1687A, G2506A and G2614A (numbered with reference to SEQ ID NO:1). In some embodiments, the oligonucleotide is about 15 to about 40nucleotides in length. In some embodiments, the oligonucleotidecomprises a label, such as, but not limited to a fluorescent label, anenzymatic label or a radioisotope.

Also provided are arrays comprising one or more oligonucleotides thatspecifically hybridize with an ERBB4 nucleic acid molecule, wherein theERBB4 nucleic acid molecule comprises a mutation selected from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1). In some embodiments, the array is amicroarray.

V. Methods of Detecting ERBB4 Mutations

Disclosed herein is the identification of novel mutations in ERBB4,which result in expression of ERBB4 protein with enhanced kinaseactivity. Seven mutations in human ERBB4 were identified, includingG949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1).

Detecting mutations in ERBB4 can be accomplished using any techniqueknown in the art. For example, the presence or absence of an ERBB4mutation can be determined by conventional methods such as gene or RNAdetection methods (for example, DNA sequencing, oligonucleotidehybridization, polymerase chain reaction (PCR) amplification withprimers specific to the mutation), or protein detection methods (forexample, immunoassays or biochemical assays to identify a mutated ERBB4protein, such as an ERBB4 with decreased kinase activity or increasedcell migration capacity). Generally, the nucleic acid sequence of theERBB4 gene or RNA in a sample can be detected by any suitable method ortechnique of detecting gene sequence. Such methods include, but are notlimited to, PCR, reverse transcriptase-PCR (RT-PCR), in situ PCR, insitu hybridization, Southern blot, Northern blot, sequence analysis,microarray analysis, or other DNA/RNA hybridization platforms.

Detection of point mutations in target nucleic acids can be accomplishedby molecular cloning of the target nucleic acid molecules and sequencingthe nucleic acid molecules using techniques well known in the art.Alternatively, amplification techniques such as PCR can be used toamplify target nucleic acid sequences directly from a genomic DNApreparation from a tumor tissue or cell sample. The nucleic acidsequence of the amplified molecules can then be determined to identifymutations. Representative primer pairs that can be used to amplify ERBB4nucleic acid from a biological sample are provided in Tables 1 and 3(SEQ ID NOs: 3-60 and 64-77). However, design and selection ofappropriate primers is well within the abilities of one of ordinaryskill in the art.

The ligase chain reaction (Wu et al., Genomics 4:560-569, 1989) andallele-specific PCR (Ruano and Kidd, Nucleic Acids Res. 17:8392, 1989)can also be used to amplify target nucleic acid sequences. Amplificationby allele-specific PCR uses primers that hybridize at their 3′ ends to aparticular target nucleic acid mutation. If the particular mutation isnot present, an amplification product is not observed. AmplificationRefractory Mutation System can also be used to detect mutations innucleic acid sequences (U.S. Pat. No. 5,595,890; Newton et al., NucleicAcids Res. 17:2503-2516, 1989). Insertions and deletions of genes canalso be detected by cloning, sequencing and amplification. In addition,restriction fragment length polymorphism probes for the gene orsurrounding marker genes can be used to score alteration of an allele oran insertion in a polymorphic fragment. Single stranded conformationpolymorphism analysis can also be used to detect base change variants ofan allele (Orita et al., Proc. Natl. Acad. Sci. USA 86:2766-2770, 1989).Other known techniques for detecting insertions and deletions can alsobe used with the claimed methods.

Mismatch detection can be used to detect point mutations in a targetnucleic acid molecule, such as ERBB4. Mismatches are hybridized nucleicacid duplexes which are not 100% complementary. The lack of totalcomplementarity can be due to deletions, insertions, inversions,substitutions or frameshift mutations. An example of a mismatch cleavagetechnique is the RNase protection method, which is described in detailin Winter et al. (Proc. Natl. Acad. Sci. USA 82:7575-7579, 1985) andMyers et al. (Science 230:1242-1246, 1985). For example, detection ofmutations in ERBB4 can involve the use of a labeled riboprobe that iscomplementary to wild-type ERBB4. The riboprobe and nucleic acidmolecule to be tested (for example, obtained from a tumor sample) areannealed (hybridized) together and subsequently digested with the enzymeRNase A, which is able to detect mismatches in a duplex RNA structure.If a mismatch is detected by RNase A, it cleaves at the site of themismatch. Thus, when the annealed RNA preparation is separated on anelectrophoretic gel matrix, if a mismatch has been detected and cleavedby RNase A, an RNA product will be seen which is smaller than thefull-length duplex RNA for the riboprobe and the mRNA or DNA. Theriboprobe need not be the full length of the target nucleic acid mRNA orgene, but can a portion of the target nucleic acid, provided itencompasses the position suspected of being mutated. If the riboprobecomprises only a segment of the target nucleic acid mRNA or gene, it maybe desirable to use a number of these probes to screen the whole targetnucleic acid sequence for mismatches if desired.

In a similar manner, DNA probes can be used to detect mismatches, forexample through enzymatic or chemical cleavage (Cotton et al., Proc.Natl. Acad. Sci. USA 85: 4397-4401, 1988; Shenk et al., Proc. Natl.Acad. Sci. USA 72:989-993, 1975). Alternatively, mismatches can bedetected by shifts in the electrophoretic mobility of mismatchedduplexes relative to matched duplexes (Cariello, Am. J. Hum. Genet.42:726-734, 1988). With either riboprobes or DNA probes, the targetnucleic acid mRNA or DNA which may contain a mutation can be amplifiedbefore hybridization. Changes in target nucleic acid DNA can also bedetected using Southern hybridization, especially if the changes aregross rearrangements, such as deletions and insertions.

Amplified nucleic acid sequences can also be screened usingallele-specific probes. These probes are nucleic acid oligomers, each ofwhich contains a region of the target nucleic acid gene harboring aknown mutation. For example, one oligomer may be about 30 nucleotides inlength, corresponding to a portion of the target gene sequence. By useof a battery of such allele-specific probes, target nucleic acidamplification products can be screened to identify the presence of apreviously identified mutation in the target gene. Hybridization ofallele-specific probes with amplified target nucleic acid sequences canbe performed, for example, on a nylon filter. Hybridization to aparticular probe under stringent hybridization conditions indicates thepresence of the same mutation in the tumor tissue as in theallele-specific probe.

The ERBB4 primer pairs disclosed herein are useful for determination ofthe nucleotide sequence of a target nucleic acid using nucleic acidamplification techniques such as the polymerase chain reaction. Thepairs of single stranded DNA primers can be annealed to sequences withinor surrounding the target nucleic acid sequence in order to primeamplification of the target sequence. Allele-specific primers can alsobe used. Such primers anneal only to particular mutant target sequence,and thus will only amplify a product in the presence of the mutanttarget sequence as a template. In order to facilitate subsequent cloningof amplified sequences, primers may have restriction enzyme sitesequences appended to their ends. Such enzymes and sites are well knownin the art. The primers themselves can be synthesized using techniqueswhich are well known in the art. Generally, the primers can be madeusing oligonucleotide synthesizing machines which are commerciallyavailable. Design of particular primers is well within the skill of theart.

Nucleic acid probes that hybridize with an ERBB4 nucleic acid molecule,such as a wild-type ERBB4 nucleic acid molecule or a mutant ERBB4nucleic acid molecule described herein, are useful for a number ofpurposes. They can be used in Southern hybridization to genomic DNA andin RNase protection assays for detecting point mutations. The probes canalso be used to detect target nucleic acid amplification products. ERBB4probes can also be used to detect mismatches with the wild type gene ormRNA using other techniques. Mismatches can be detected using eitherenzymes (e.g., S1 nuclease), chemicals (e.g., hydroxylamine or osmiumtetroxide and piperidine), or changes in electrophoretic mobility ofmismatched hybrids as compared to totally matched hybrids (Novack etal., Proc. Natl. Acad. Sci. USA 83:586, 1986).

Mutations in nucleic acid molecules can also be detected by screeningfor alteration of the corresponding protein. For example, monoclonalantibodies immunoreactive with a target gene product can be used toscreen a tissue, for example an antibody that is known to bind to aparticular mutated position of the gene product (protein). For example,a suitable antibody may be one that binds to a deleted exon or thatbinds to a conformational epitope comprising a deleted portion of thetarget protein. Lack of cognate antigen would indicate a mutation. Suchimmunological assays can be accomplished using any convenient formatknown in the art, such as Western blot, immunohistochemical assay andenzyme-linked immunosorbent assay (ELISA). In some embodiments, theERBB4 amino acid mutation is selected from E317K, E452K, E542K, R544W,E563K, E836K and E872K (numbered with reference to SEQ ID NO: 2).

VI. Arrays

In particular embodiments provided herein, arrays can be used toevaluate the presence or absence of mutations in ERBB4. In someexamples, the array comprises an oligonucleotide that specificallyhybridizes with an ERBB4 nucleic acid molecule comprising a mutationselection from G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A(numbered with reference to SEQ ID NO: 1). Oligonucleotides thatspecifically hybridize with an ERBB4 nucleic acid comprising a mutationdo not hybridize to WT ERBB4, or hybridization of the oligonucleotide toWT ERBB4 is significantly weaker than hybridization to the mutant ERBB4.In some embodiments the array comprises two or more oligonucleotidesthat specifically hybridize with an ERBB4 nucleic acid comprising amutation selected from G949A, G1354A, G1624A, C1630T, G1687A, G2506A andG2614A (numbered with reference to SEQ ID NO: 1). In other embodiments,the array comprises oligonucleotides that specifically hybridize withERBB4 nucleic acid molecules comprising each mutation of G949A, G1354A,G1624A, C1630T, G1687A, G2506A and G2614A (numbered with reference toSEQ ID NO: 1). In some examples, the array further comprises otheroligonucleotides, such as control oligonucleotides or oligonucleotidesthat specifically hybridize with WT ERBB4 or other mutant ERBB4 nucleicacid molecules. Exemplary control oligonucleotide probes include GAPDH,actin, and YWHAZ.

The oligonucleotide probes can further include one or more detectablelabels, to permit detection of hybridization signals between the probeand target sequence (such as one of the mutant ERBB4 nucleic acidmolecules).

Array Substrates

The solid support of the array can be formed from an organic polymer.Suitable materials for the solid support include, but are not limitedto: polypropylene, polyethylene, polybutylene, polyisobutylene,polybutadiene, polyisoprene, polyvinylpyrrolidine,polytetrafluoroethylene, polyvinylidene difluoroide,polyfluoroethylene-propylene, polyethylenevinyl alcohol,polymethylpentene, polycholorotrifluoroethylene, polysulformes,hydroxylated biaxially oriented polypropylene, aminated biaxiallyoriented polypropylene, thiolated biaxially oriented polypropylene,etyleneacrylic acid, thylene methacrylic acid, and blends of copolymersthereof (see U.S. Pat. No. 5,985,567).

In general, suitable characteristics of the material that can be used toform the solid support surface include: being amenable to surfaceactivation such that upon activation, the surface of the support iscapable of covalently attaching a biomolecule such as an oligonucleotidethereto; amenability to “in situ” synthesis of biomolecules; beingchemically inert such that at the areas on the support not occupied bythe oligonucleotides are not amenable to non-specific binding, or whennon-specific binding occurs, such materials can be readily removed fromthe surface without removing the oligonucleotides.

In one example, the solid support surface is polypropylene.Polypropylene is chemically inert and hydrophobic. Non-specific bindingis generally avoidable, and detection sensitivity is improved.Polypropylene has good chemical resistance to a variety of organic acids(such as formic acid), organic agents (such as acetone or ethanol),bases (such as sodium hydroxide), salts (such as sodium chloride),oxidizing agents (such as peracetic acid), and mineral acids (such ashydrochloric acid). Polypropylene also provides a low fluorescencebackground, which minimizes background interference and increases thesensitivity of the signal of interest.

In another example, a surface activated organic polymer is used as thesolid support surface. One example of a surface activated organicpolymer is a polypropylene material aminated via radio frequency plasmadischarge. Such materials are easily utilized for the attachment ofnucleotide molecules. The amine groups on the activated organic polymersare reactive with nucleotide molecules such that the nucleotidemolecules can be bound to the polymers. Other reactive groups can alsobe used, such as carboxylated, hydroxylated, thiolated, or active estergroups.

Array Formats

A wide variety of array formats can be employed in accordance with thepresent disclosure. One example includes a linear array ofoligonucleotide bands, generally referred to in the art as a dipstick.Another suitable format includes a two-dimensional pattern of discretecells (such as 4096 squares in a 64 by 64 array). As is appreciated bythose skilled in the art, other array formats including, but not limitedto slot (rectangular) and circular arrays are equally suitable for use(see U.S. Pat. No. 5,981,185). In some examples, the array is amulti-well plate. In one example, the array is formed on a polymermedium, which is a thread, membrane or film. An example of an organicpolymer medium is a polypropylene sheet having a thickness on the orderof about 1 mil. (0.001 inch) to about 20 mil., although the thickness ofthe film is not critical and can be varied over a fairly broad range.The array can include biaxially oriented polypropylene (BOPP) films,which in addition to their durability, exhibit low backgroundfluorescence.

The array formats of the present disclosure can be included in a varietyof different types of formats. A “format” includes any format to whichthe solid support can be affixed, such as microtiter plates (e.g.multi-well plates), test tubes, inorganic sheets, dipsticks, and thelike. For example, when the solid support is a polypropylene thread, oneor more polypropylene threads can be affixed to a plastic dipstick-typedevice; polypropylene membranes can be affixed to glass slides. Theparticular format is, in and of itself, unimportant. All that isnecessary is that the solid support can be affixed thereto withoutaffecting the functional behavior of the solid support or any biopolymerabsorbed thereon, and that the format (such as the dipstick or slide) isstable to any materials into which the device is introduced (such asclinical samples and hybridization solutions).

The arrays of the present disclosure can be prepared by a variety ofapproaches. In one example, oligonucleotide sequences are synthesizedseparately and then attached to a solid support (see U.S. Pat. No.6,013,789). In another example, sequences are synthesized directly ontothe support to provide the desired array (see U.S. Pat. No. 5,554,501).Suitable methods for covalently coupling oligonucleotides to a solidsupport and for directly synthesizing the oligonucleotides onto thesupport are known to those working in the field; a summary of suitablemethods can be found in Matson et al. (Anal. Biochem. 217:306-10, 1994).In one example, the oligonucleotides are synthesized onto the supportusing conventional chemical techniques for preparing oligonucleotides onsolid supports (such as see International application publications WO85/01051 and WO 89/10977, or U.S. Pat. No. 5,554,501).

A suitable array can be produced using automated means to synthesizeoligonucleotides in the cells of the array by laying down the precursorsfor the four bases in a predetermined pattern. Briefly, amultiple-channel automated chemical delivery system is employed tocreate oligonucleotide probe populations in parallel rows (correspondingin number to the number of channels in the delivery system) across thesubstrate. Following completion of oligonucleotide synthesis in a firstdirection, the substrate can then be rotated by 90° to permit synthesisto proceed within a second (2°) set of rows that are now perpendicularto the first set. This process creates a multiple-channel array whoseintersection generates a plurality of discrete cells.

The oligonucleotides can be bound to the polypropylene support by eitherthe 3′ end of the oligonucleotide or by the 5′ end of theoligonucleotide. In one example, the oligonucleotides are bound to thesolid support by the 3′ end. However, one of skill in the art candetermine whether the use of the 3′ end or the 5′ end of theoligonucleotide is suitable for bonding to the solid support. Ingeneral, the internal complementarity of an oligonucleotide probe in theregion of the 3′ end and the 5′ end determines binding to the support.

In particular examples, the oligonucleotide probes on the array includeone or more labels, that permit detection of oligonucleotideprobe:target sequence hybridization complexes.

VII. Use of ERBB4 for Prognosis and Therapy

It is disclosed herein that ERBB4 is highly mutated in melanoma tumors.The disclosed ERBB4 somatic mutations result in increased ERBB4 kinaseactivity, transformation capacity and anchorage-independent growth. Thehigh frequency of mutations identified in ERBB4, their co-localization,and the identification of two identical missense mutations (E452K andE872K) in multiple MM samples indicates these mutations play a role intumorigenesis. In addition, the ERBB4 mutations disclosed herein exhibitligand-independent basal phosphorylation, providing evidence that thesemutations are oncogenic. Accordingly, the identified mutations in ERBB4predict a poor prognosis for patients with melanoma. In someembodiments, a poor prognosis is an increase in the likelihood of death.In some embodiments, a poor prognosis is an increase in metastasis.

The detection of one or more ERBB4 mutations selected from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1) can be used as a clinical tool to determinethe prognosis of a patient with melanoma. Since these mutations areoncogenic and play a role in tumorigenesis of MM, a poor prognosis isindicated when one or more of the mutations is detected in a sample froma subject diagnosed with melanoma. Detection of one or more of thesemutations can also be used as a tool for determining an appropriatetherapy for a subject with melanoma. The presence of one or more ofthese mutations indicates the subject is a candidate for treatment witha kinase inhibitor, such an EGFR family inhibitor, or more particularly,an ERBB4-specific inhibitor. In some examples, the ERBB4 mutationintroduces an amino acid change selected from E317K, E452K, E542K,R544W, E563K, E836K and E872K (numbered with reference to SEQ ID NO: 2).

It is also disclosed herein that mutations in ERBB4 activate thePI3K/AKT pathway, as indicated by increased phosphorylation of AKT inmelanoma cells harboring the disclosed ERBB4 mutations. Thus, thepresence of one or more ERBB4 mutations indicates the subject is acandidate for treatment with an inhibitor of the PI3K/AKT pathway, suchas an inhibitor of PI3K or AKT. In some embodiments, the method ofselecting a patient as a candidate for treatment with an ERBB4 and/orPI3K/AKT pathway inhibitor further includes treating the subject with anERBB4 inhibitor, a PI3K/AKT pathway inhibitor, or both.

The finding that the presence of prognosis-associated ERBB4 mutationsselected from G949A, G1354A, G1624A, C1630T, G1687A, G2506A and G2614A(numbered with reference to SEQ ID NO: 1) result in an increase inkinase activity, transformation capacity and/or anchorage-independentgrowth indicates that compounds that inhibit (such as decrease kinaseactivity of) ERBB4 will be useful as therapeutic agents for thetreatment of melanoma. Thus, provided herein is a method of identifyingtherapeutic agents for the treatment of melanoma, comprising screeningcandidate agents to select an agent that inhibits activity (such askinase activity) or expression of ERBB4.

In some embodiments, screening comprises contacting the candidate agentswith cells that express ERBB4 and detecting any change in activity orexpression of ERBB4. The ERBB4 expressing cells can be primary cellsobtained from a subject diagnosed with melanoma, immortalized ortransformed cells obtained from a melanoma patient, or the cells can becommercially available immortalized cell lines. In some embodiments, thecells express wild-type ERBB4. In other embodiments, the cells expressmutant ERBB4, such as ERBB4 with a mutation selection from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1). In some examples, a cell line is transfectedwith an expression vector encoding wild-type or mutant ERBB4. In otherexamples, primary tumor cells expressing mutant ERBB4 are evaluated. Ineither case, the cells are either untreated or treated with a candidateagent and ERBB4 kinase activity is measured, for example byincorporation of radiolabeled ATP. A decrease in ERBB4 activity in thetreated cells, compared to the untreated cells, indicates the candidateagent is a therapeutic agent for melanoma.

In some embodiments, a decrease in kinase activity of ERBB4 followingtreatment with the candidate agent identifies the agent as a therapeuticagent for the treatment of melanoma. In some embodiments, thetherapeutic agent decreases kinase activity of ERBB4 at least 2-fold, atleast 3-fold, at least 4-fold or at least 5-fold relative to untreatedcells. Methods of screening candidate agents to identify therapeuticagents for the treatment of disease are well known in the art. In oneembodiment, screening comprises a high-throughput screen. In anotherembodiment, candidate agents are screened individually.

Given the finding that mutations in ERBB4 result in activation of thePI3K/AKT pathway, provided herein is a method of identifying therapeuticagents for the treatment of melanoma, comprising screening candidateagents to select an agent that inhibits activity or expression of amember of the PI3K/AKT pathway, such as PI3K or AKT. In someembodiments, screening comprises contacting the candidate agents withcells that express mutant ERBB4 and detecting any change in activity orexpression of a member of the PI3K/AKT pathway. The mutant ERBB4expressing cells can be primary cells obtained from a subject diagnosedwith melanoma, immortalized or transformed cells obtained from amelanoma patient, or the cells can be commercially availableimmortalized cell lines. In some embodiments, the cells express ERBB4with a mutation selection from G949A, G1354A, G1624A, C1630T, G1687A,G2506A and G2614A (numbered with reference to SEQ ID NO: 1). In someexamples, a cell line is transfected with an expression vector encodingmutant ERBB4. In other examples, primary tumor cells expressing mutantERBB4 are evaluated. In either case, the cells are either untreated ortreated with a candidate agent and PI3K/AKT activity is measured. Insome examples, PI3K/AKT activity is measured by detecting the level ofAKT phosphorylation. A decrease in PI3K/AKT activity in the treatedcells, compared to the untreated cells, indicates the candidate agent isa therapeutic agent for melanoma.

The candidate agents can be any type of molecule, such as, but notlimited to nucleic acid molecules, proteins, polypeptides, antibodies,lipids, small molecules, chemicals, cytokines, chemokines, hormones, orany other type of molecule that may alter ERBB4 or PI3K/AKT activityeither directly or indirectly. In some embodiments, the candidate agentsare small molecules, polypeptides (such as antibodies) or nucleic acidmolecules (such as antisense compounds, including antisenseoligonucleotides, siRNAs or ribozymes).

The following examples are provided to illustrate certain particularfeatures and/or embodiments. These examples should not be construed tolimit the disclosure to the particular features or embodimentsdescribed.

EXAMPLES Example 1 Experimental Procedures

This example describes the materials and methods used for theexperiments described in Examples 2-6.

Amplification, Sequencing and Mutational Analysis of ERBB4

Metastatic melanoma samples and their matched normal samples wereobtained according to standard procedures. Genomic DNA was isolatedusing DNeasy™ Blood & Tissue kit (Qiagen, Valencia, Calif.). For allsamples, matching between germline and tumor DNA was verified by directsequencing of 26 single nucleotide polymorphisms (SNPs) at 24 loci. Thetissue and melanoma cell lines used in the Examples below are alsodescribed in Palavalli et al. (Nat. Genet. 41:518-520, 2009).

PCR and sequencing primers were designed using Primer 3 (availableonline at frodo.wi.mit.edu/cgi-bin/primer3/primer3_www.cgi) andsynthesized by Invitrogen (Carlsbad, Calif.). The primers used for PCRamplification of the whole coding region of ERBB4 are shown in Table 1(CCDS accession CCDS2394.1; GenBank Accession No. NM_(—)005235; SEQ IDNO: 1). The coding region of ERBB4 was sequenced using a primer with thefollowing sequence: GTAAAACGACGGCCAGT (SEQ ID NO: 61). PCRamplification, sequencing and analysis were performed as previouslydescribed (Samuels et al., Science 304:554, 2004). Briefly, PCR productswere purified using exonuclease (Epicentre Biotechnologies, Madison,Wis.) and shrimp alkaline phosphatase (USB Corporation, Cleveland,Ohio). Products were purified with rehydrated Sephadex™ G-50 powder (GEHealthcare, Piscataway, N.J.) and cycle sequencing was carried out usingBigDye Terminator™ v3.1 Cycle Sequencing kit (Applied Biosystems, FosterCity, Calif.). Sequence data was collected on an ABI3730x1 (AppliedBiosystems, Foster City, Calif.).

The kinase domain mutation screen was analyzed using Consed (Gordon etal., Genome Res. 8(3):195-202, 1998). Variants were called usingPolyphred 6.11 (Bhangale et al., Nat. Genet. 38(12):1457-1462, 2006) andDIPDetector, an indel detector for improved sensitivity in findinginsertions and deletions.

Sequence traces of the secondary screen were analyzed using the MutationSurveyor software package (SoftGenetics, State College, Pa.).

TABLE 1 Primers used for PCR amplification of the ERBB4 coding regionERBB4 SEQ ID SEQ ID Exon Forward Primer NO: Reverse Primer NO: Exon 1GGAAATAGCTGCACAG 3 GTAAAACGACGGCCAG 32 TCCG TATGGGTGAAGAGGGC AGG Exon 2AGAACTGGGATAGGCT 4 GTAAAACGACGGCCAG 33 TGTGG TTTCCAGGTATCAGCA CACAGGExon 3 GTAAAACGACGGCCAG 5 TGCCTTAGAGTGTTCC 34 TAAGCCAATTCTTTAGA TCAATGATATGATATGG Exon 4 TCTTGGCTATTAGCAAC 6 GTAAAACGACGGCCAG 35 ATGACTCTCAATGAATGCAATCA AAGTTCAA Exon 5 GTAAAACGACGGCCAG 7 CCAAAGCAAATCAACC 36TAAATCCTCATAAAGG ACAAG AGCAGGAG Exon 6 GTAAAACGACGGCCAG 8GGAATGACTTTGAGGA 37 TTGAATTGAGTCAAAG GGGC ACAGGGTG Exon 7TTTGGAAACACACATG 9 GTAAAACGACGGCCAG 38 ACTCTTAAA TTTTGCTATGAAACTTTACACAAATCA Exon 8 GTGGAGCAGTAACCAA 10 GTAAAACGACGGCCAG 39 GCAAGTGTGTGGGTAGGTTTG GTTGTG Exon 9 AAAGCAGAACCAGTAG 11 GTAAAACGACGGCCAG 40TGAATGTTG TGGTGAAACTCTTCAG CTTCCAG Exon 10 GTAAAACGACGGCCAG 12TCTCCTGACCTCATGA 41 TCCTCCTCCACATCTAG TCCAC CACAG Exon 11GTAAAACGACGGCCAG 13 TACCTCACACCATCAT 42 TCCTTTCTCACTTCCCA CGGAG ACTTTCExon 12 GTAAAACGACGGCCAG 14 GAGCAACAATTCTGAC 43 TTTGATTCAGTTTCCAT CGGATTTATACACCA Exon 13 GTAAAACGACGGCCAG 15 GAATGGCGTGAACCCA 44TTAGGCCACCAAAGTC GG ATTTGC Exon 14 GTAAAACGACGGCCAG 16 CCCATGGCATCCTGTA45 TTGATGCTCCTGGCACA AGTAG TAGAG Exon 15 TCTTAGAGGAAGATTT 17GTAAAACGACGGCCAG 46 GCCACC TCATTTCAGAGATGGT ACCAGGG Exon 16GCTTCCCATGTTCTTCC 18 GTAAAACGACGGCCAG 47 TCC TAAGTAAGAAAGTTGG CTTGAGAAGGExon 17 TGTGGATAATGTCTTGT 19 GTAAAACGACGGCCAG 48 ACAACTGCTTTCACAAGCTTTGTTT AACGGAC Exon 18 GGTTGTCAAGGCAAAC 20 GTAAAACGACGGCCAG49 CAAG TAGACTGTATCCGTCC CAGCTC Exon 19 AAGCAGACAACAAAGT 21GTAAAACGACGGCCAG 50 TGCAGAG TTCTAGGCAGACAGTT GTGAAGC Exon 20GTAAAACGACGGCCAG 22 TTTGGCACCTAGTCAA 51 TTCAGCACCATTAGTAC TTCAA AATCCAAExon 21 GTAAAACGACGGCCAG 23 AGGCAAATGGTAGAAC 52 TGCACTTCCAACTGAA CAAGGGGCTAAG Exon 22 GTAAAACGACGGCCAG 24 TAACTGCTTTAGGAAA 53 TAGGCCAGCCCAAAGATTAGGCTTATC CTC Exon 23 TGATTGGTGTTTGGATT 25 GTAAAACGACGGCCAG 54 GACCTCAAAGAGGCGTTCAT ATGTTCC Exon 24 GTAAAACGACGGCCAG 26 TGTTTGTGGTCCTTTCC55 TGAGTCGTTTCTTTCAC ACAG TAGCTTGC Exon 25 TAGGTTTCTTAATGGCC 27GTAAAACGACGGCCAG 56 GGTG TGGCATCACATTGATT TGAGCTA Exon 26TGCTTAGGAAGCTTCAC 28 GTAAAACGACGGCCAG 57 TGTTG TTAACTCACTGTTGGC AAAGGCExon 27 TGGCTTTGATATCCTTG 29 GTAAAACGACGGCCAG 58 TGGC TCAGCTATCTGGCAATTTCTATTCTG Exon 28 CCATATGCAGAAGAGA 30 GTAAAACGACGGCCAG 59 CAAATGCTAGGTAGTCTGGGTGC TGAAGG Exon 28 TGAATCCAGTGGAGGA 31 GTAAAACGACGGCCAG 60GAACC TGACCACCAGAGAAAG AGAGGG

Construction of Wild-Type and Mutant ERBB4 Expression Vectors

Human ERBB4 (GenBank Accession No. NM_(—)005235; SEQ ID NO: 1) wascloned by PCR using PHUSION™ Hot Start High-Fidelity DNA Polymerase (NewEngland Biolabs, Inc., Ipswich, Mass.) using a clone purchased from OpenBiosystems (clone ID #8327667) and cloned with the following primers:

CGGCTCTAGAGCCACCATGAAGCCGGCGAC (SEQ ID NO: 62)ATCGGCGGCCGCTTACACCACAGTATTCCGG (SEQ ID NO: 63)

The PCR product was cloned into the mammalian expression vectorpCDF-MCS2-EF1-Puro™ (Systems Biosciences, Inc., Mountain View, Calif.)via the XbaI and NotI restriction sites. The E317K, E452K, E542K, R544W,E563K, K751M, E836K, and E872K point mutants were made using Fusion PCRfor site-directed mutagenesis.

Cell Culture and Transient Expression

Metastatic melanoma tumor lines were maintained according to standardmethods (see Chappell et al., Cancer Res. 59:59-62, 1999). HEK 293Tcells and NIH 3T3 cells were purchased from the American Type CultureCollection (ATCC) (Manassas, Va.) and maintained in complete Dulbecco'sModified Eagles Medium (DMEM) supplemented with 10% Fetal Bovine Serum(FBS), 1× nonessential amino acids, 2 mM L-glutamine, and 0.75% sodiumbicarbonate. HEK 293T cells were transfected with Lipofectamine™ 2000reagent (Invitrogen, Carlsbad, Calif.) at a 6:1 ratio with DNA (μl/μg)using 3-5 μg of plasmid DNA.

Immunoprecipitation and Western Blotting

Transfected cells were washed 3× in PBS and lysed using 0.5 ml 1% NP-40lysis buffer (1% NP-40, 50 mM Tris-HCl pH 7.5, 150 mM NaCl, completeprotease inhibitor tablet, EDTA-free (Roche, Indianapolis, Ind.), 1 μMsodium orthovanadate, 1 mM sodium fluoride, and 0.1% β-mercaptoethanol)per T-75 flask for 20 minutes on ice. Lysed cells were scraped andtransferred into a 1.5 mL microcentrifuge tube. Extracts werecentrifuged for 10 minutes at 14,000 rpm at 4° C. Supernatant (450 μl)was immunoprecipitated overnight using 20 μl of anti-ERBB4agarose-conjugated beads (Santa Cruz Biotechnology, Inc., Santa Cruz,Calif.). The immunoprecipitates were washed and subjected to SDS-PAGEand western blotting according to standard methods (see Samuels et al.,Science 304:554, 2004). The primary antibodies used in these experimentswere anti-ERBB4 (Santa Cruz Biotechnology, Santa Cruz, Calif.),anti-P-ERBB4 (Y1162) (Abgent, San Diego, Calif.), anti-P-ERBB4 (Y1284)(Cell Signaling, Danvers, Mass.), anti-PY20 (Zymed-Invitrogen,),anti-P-ERK1/2 (T202/Y204), anti-ERK1/2, anti-P-AKT (S473), anti-AKT(Cell Signaling), anti-P-STAT5A/B (Y694/Y699) (UpstateBiotech-Millipore), anti-STATS (Cell Signaling) and anti-α-tubulin(Calbiochem-EMD Biosciences, Gibbstown, N.J.).

ERBB4 Phosphorite-Specificantibody Analysis

ERBB4 was immunoprecipitated as described above and subjected toSDS-PAGE. Primary phospho-antibodies were pre-incubated overnight withthe relevant competitive phospho-peptides (pPep Y1162-Abgent #BP3122a,pPep Y1284-Cell Signaling #1022). Following blocking/competition, theantibody/peptide mixture was diluted into blocking buffer and westernblotting was performed as described above.

Pooled Stable Expression

To make lentivirus, ERBB4 constructs were co-transfected into HEK 293Tcells seeded at 1.5×10⁶ per T75 flask with pVSV-G and pFIV-34N helperplasmids (System Biosciences, Mountain View, Calif.) usingLipofectamine™ 2000. Virus-containing conditioned media was harvested48-60 hours after transfection, filtered, aliquoted and stored at −80°C. ERBB4 lentivirus was used to make SK-MeI-2 and NIH 3T3 stable clones.

SK-MeI-2 cells (National Cancer Institute, Division of Cancer Treatment,Developmental Therapeutics Program, Frederick, Md.) were grown inRPMI-1640 (Lonza, Walkersville, Md.) supplemented with 10% fetal bovineserum (HyClone, Logan, Utah). NIH 3T3 cells were grown in DMEMsupplemented with 10% FBS, 2 mM L-glutamine, 1× non-essential aminoacids, and 0.75% sodium bicarbonate. Sk-Mel-2 and NIH 3T3 cells wereseeded at 1.5×10⁶ cells per T75 flask 24 hours prior to infection.Lentivirus for ERBB4 (WT, E317K, E452K, E542K, R544W, E563K, K751M,E836K, and E872K point mutants) and empty vector control were dilutedwith equal volume of normal complete medium in the presence of 8 μg/mlpolybrene. Cells were incubated for 24 hours in the presence of virusfollowed by changing of the medium to normal complete medium for anadditional 24 hours. Lentivirus-infected cells were then selected for byaddition of complete medium containing 3 μg/ml puromycin for SK-MeI-2cells or 2 μg/ml puromycin for NIH 3T3 cells and allowed to incubate for3 days. Stable expression of ERBB4 proteins (WT and mutants) wasdetermined by SDS-PAGE analysis followed by immunoblotting withanti-ERBB4 and anti-tubulin to show equivalent expression among pools.

Lentiviral shRNA

Constructs for stable depletion of ERBB4 were obtained from OpenBiosystems (Huntsville, Ala.). Negative control constructs in the samevector system (pLKO.1 vector alone and scrambled shRNA) were obtainedfrom Addgene (Cambridge, Mass.). To prepare transient virus stocks,1.5×10⁶ HEK 293T cells were plated in T75 flasks. The next day, thecells were co-transfected with shRNA constructs (3 μg), together withpHR′8.2ΔR and pCMV-VSV-G helper constructs (3 μg and 0.3 μg,respectively), using Lipofectamine™ 2000 (Invitrogen). The media werechanged the next day, and the following day, and virus-containing mediawere harvested. The viral stocks were centrifuged and filtered to removeany non-adherent HEK 293T cells.

Next, MM lines (2T, 7T, 17T, 31T and 63T) were infected with shRNAlentiviruses for each condition (vector and scrambled controls and threeindependent ERBB4-specific shRNAs). To do this, cells were plated atsub-confluent densities. The next day, cells were infected with acocktail of 1 ml virus-containing medium, 1 ml regular medium and 8μg/ml polybrene. The medium was changed one day post-infection, andselective medium was added two days post-infection (2 μg/ml puromycinfor all cells). After three days of puromycin selection, themock-infected cells had all died. Stably infected pooled clones weretested in functional assays.

To rescue shRNA-mediated knock-down of ERBB4 in melanoma cell lines, thenon-targetable ERBB4 lentivirus was made as described above and used toinfect the melanoma cell line 17T. After infection, cells were given 48to 72 hours to recover from infection prior to testing in functionalassays.

Proliferation and Growth Inhibition Assays

To examine growth potential, melanoma cell lines (2T, 7T, 17T, 31T and63T) stably infected with either vector or scrambled controls orERBB4-specific shRNAs were seeded into 96-well plates at 2,500 cells perwell and incubated for 13-17 days. Samples were analyzed every 48 hoursby lysing cells in 50 μl 0.2% SDS/well and incubating for 2 hours at 37°C. prior to addition of 150 μl/well of SYBR Green I solution (1:750 SYBRGreen I (Invitrogen-Molecular Probes) diluted in dH₂0).

The effects of tyrosine kinase inhibitors (TKIs) on the proliferation ofmelanoma cell lines were tested by seeding 96-well plates at 5,000cells/well in the presence or absence of serum-containing media andincubated for 24 hours prior to addition of TKIs. Increasingconcentrations of lapatinib (Tykerb-GlaxoSmithKline) were added to eachwell in four replicates with DMSO as negative control. Plates wereanalyzed 72 hours post-addition of TKIs using the SYBR Green Iproliferation assay described above.

To further test TKIs on melanoma cell lines, 96-well plates were seededat 5,000 cells per well and incubated 24 hours prior to addition of TKIs(e.g. lapatinib) at concentrations from 10 nM to 30 μM. Once inhibitorswere added, cells were incubated for 72 hours at 37° C. Cells were thenanalyzed according to previously described methods (Rusnak et al., Mol.Cancer. Ther. 1:85-94, 2001). Plates were read at 650 nm on a MolecularDevices (Spectra Max) Plate Reader and analyzed using SoftMax v5 andGraphPad Prism v5.

Soft Agar Assay

SK-MeI-2 pooled ERBB4 clones were plates in duplicate at 1000 cells/welland NIH 3T3 pooled ERBB4 clones were plated in duplicate at 5000cells/well in top plugs consisting of sterile 0.33% Bacto-Agar (BD,Sparks, Mo.) and 10% FBS (HyClone, Logan, Utah) in a 24-well plate. Thelower plug contained sterile 0.5% Bacto-Agar and 10% FBS. After twoweeks, the colonies were photographed and counted.

NIH 3T3 Transformation Assay

Each plasmid (150 ng) was transfected into NIH 3T3 cells cultured in12-well plates by the calcium phosphate precipitation method.Twenty-four hours after transfection, 5% of transfected cells weretransferred into T25 flasks and cultured for 10 days in normal growthmedium. The cells were stained with Hema3 (Sigma St. Louis, Mo.) andanalyzed for the presence of foci.

Analysis of ERBB4 Kinase Activity

HEK 293T cells were transiently transfected with ERBB4 (WT, E317K,E452K, E542K, R544W, E563K, E836K, E872K and kinase-dead K751M) or emptyvector and incubated for 18-24 hours at 37° C. in the presence (10%) orabsence (0.5%) of serum-containing medium prior to immunoprecipitation.Cells were harvested and approximately 3 mg of lysate wasimmunoprecipitated as described above and subjected to a kinase assay.Immune complexes were washed three times in lysis buffer followed by twowashes in kinase buffer (20 mM HEPES pH 7.4, 50 mM NaCl, 3 mM MnCl₂, 20mM MgCl₂, 1 mM sodium orthovanadate, 1 mM sodium fluoride, and 1×complete protease inhibitor tablet). Immune complexes were resuspendedin 50 μl kinase buffer and 10 μl was incubated in the presence of[γ-³²P]ATP (3 μCi per reaction) for 15 minutes at 37° C. Kinasereactions were stopped by the addition of 2×SDS sample buffer andphosphorylated samples were resolved on 8% tris-glycine gels. Gels werefixed in a 50% methanol/7% acetic acid solution, washed three times indH₂O then stained for 1 hour in GelCode™ Blue stain (Pierce) followed bydestaining for an additional hour. Gels were dried prior toautoradiography.

Immunoblot Quantitation Analysis

Scanned films from western blot analysis of SDS-PAGE were analyzed usingImageJ (NIH software). Individual bands were quantitated and plots weregenerated to determine the intensities in each band. The data was thenexported to Microsoft Excel and analyzed further for phospho:totalratios of protein.

Flow Cytometry Analysis

Melanoma cells were seeded into T-25 flasks at densities of 3×10⁵ cellsper flask in normal complete T2 medium and incubated at 37° C. for 24hours prior to addition of lapatinib. Lapatinib or vehicle was added for72 hours at a concentration of 5 μM. Cells were then harvested for FACSanalysis by first removing the medium into a new conical tube followedby trypsinization of attached cells in T-25 flasks. Trypsinized cellsand those from the medium were combined and washed in ice-cold PBS.Cells were collected by centrifugation at 1,000 rpm at 4° C. Ice-cold70% ethanol was added to cell pellets and allowed to fix overnight at 4°C. followed by washing in ice-cold PBS. DNase-free RNase (Roche) wasadded to cells resuspended in 0.5-1 ml PBS and incubated at 37° C. for30 minutes before adding 50-100 μl of propidium iodide (PI-0.5 mg/ml)(Roche). Cellular DNA content was analyzed on Becton DickinsonFACSCalibur™ using CellQuest™ software.

X-ray crystal structure assembly

The X-ray crystal structures of the ERBB4 extracellular and kinasedomains were used as templates in the program SWISS-MODEL (Guex andPeitsch, Electrophoresis 18:2714-2723, 1997). Location of EGFR and ERBB2mutations in the crystal were found by aligning the protein sequencesfor EGFR, ERBB2, ERBB3, and ERBB4 using ClustalW (Guex and Peitsch,Electrophoresis 18:2714-2723, 1997). Previously identified mutations inEGFR and ERBB2 were matched to the sequence of ERBB4 using the ClustalWalignment.

Statistical Analysis

To determine whether the ratio of nonsynonymous to synonymous mutationsobserved was statistically significant, the exact binomial test wasused, with an expected ratio of 2.5:1. All the statistical calculationswere performed in the R statistical environment (available online on theWorld Wide Web at r-project.org) (Sjoblom et al., Science 314:268-274,2006). Further statistical analyses were performed using Microsoft Excelto generate p-values to determine significance (two-tailed t-test).Inhibition curves (IC₅₀) were analyzed and plotted using GraphPad Prismv5.

Example 2 High-Throughput DNA Sequence Analysis of the PTK Family in MM

This example describes the identification of somatic mutations inmembers of the PTK family, including ERBB4, in patients with melanoma.Kinase mutations have been previously identified by sequencing genesencoding these domains (Bardelli et al., Science 300:949, 2003; Davieset al., Nature 417(6892):949-954, 2002; Greenman et al., Nature446:153-158, 2007; Samuels et al., Science 304:554, 2004). Thus, PTKswere evaluated herein to determine if they are genetically altered inMM. Initially, the kinase domain coding exons of this gene superfamilywere analyzed in 29 MM samples (Table 2). A total of 593 exons wereextracted from genomic databases. These exons were amplified bypolymerase chain reaction (PCR) from cancer genomic DNA samples usingthe primers listed in Table 1 and directly sequenced with dye terminatorchemistry.

TABLE 2 Tyrosine Kinase genes analyzed CCDS Ref Seq accession andaccession and amplimer amplimer number number Gene Name Gene DescriptionCCDS35165.1 NM_007313.2 ABL1/ABL v-abl Abelson murine leukemia viraloncogene homolog 1 CCDS30947.1 NM_007314.2 ABL2/ARG v-abl Abelson murineleukemia viral oncogene homolog 2 (arg, Abelson-related gene)CCDS33928.1 NM_005781.4 ACK1/TNK2 tyrosine kinase, non-receptor, 2CCDS33172.1 NM_004304.3 ALK anaplastic lymphoma kinase (Ki-1)CCDS12575.1 NM_021913.3 AXL AXL receptor tyrosine kinase CCDS5982.1NM_001715.2 BLK B lymphoid tyrosine kinase CCDS14168.1 NM_203281.2 BMXBMX non-receptor tyrosine kinase CCDS13524.1 NM_005975.2 BRK/PTK6 PTK6protein tyrosine kinase 6 CCDS14482.1 NM_000061.1 BTK Brutonagammaglobulinemia tyrosine kinase CCDS4302.1 NM_005211.2 CSF1R colonystimulating factor 1 receptor, formerly McDonough feline sarcoma viral(v-fms) oncogene homolog CCDS10269.1 NM_004383.1 CSK c-src tyrosinekinase CCDS4690.1 NM_001954.4 DDR1 discoidin domain receptor family,member 1 CCDS1241.1 NM_006182.2 DDR2 discoidin domain receptor family,member 2 CCDS5514.1 NM_005228.3 EGFR epidermal growth factor receptor(erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)CCDS5884.1 NM_005232.3 EPHA1 ephrin receptor EphA1 CCDS169.1 NM_004431.2EPHA2 ephrin receptor EphA2 CCDS2922.1 NM_005233.5 EPHA3 ephrin receptorEphA3 isoform a precursor CCDS2447.1 NM_004438.3 EPHA4 ephrin receptorEphA4 CCDS3514.1 NM_182472.1 EPHA5 ephrin receptor EphA5 isoform b N/ANM_001080448.2 EPHA6 EPH receptor A6 isoform a CCDS5031.1 NM_004440.2EPHA7 ephrin receptor EphA7 CCDS30626.1 NM_001006943.1 EPHA8 EPHreceptor A8 isoform 2 precursor CCDS425.1 NM_173641.2 EPHA10 EPHreceptor A10 isoform 2 N/A NM_004441.3 EPHB1 ephrin receptor EphB1precursor CCDS230.1 NM_004442.6 EPHB2 ephrin receptor EphB2 isoform 2precursor CCDS3268.1 NM_004443.3 EPHB3 ephrin receptor EphB3 precursorCCDS5706.1 NM_004444.4 EPHB4 ephrin receptor EphB4 precursor CCDS5873.1NM_004445.2 EPHB6 ephrin receptor EphB6 precursor CCDS32642.1NM_004448.2 ERBB2 v-erb-b2 erythroblastic leukemia viral oncogenehomolog 2, neuro/glioblastoma derived oncogene homolog (avian)CCDS31833.1 NM_001982.2 ERBB3 v-erb-b2 erythroblastic leukemia viraloncogene homolog 3 (avian) CCDS2394.1 NM_005235.2 ERBB4 v-erb-aerythroblastic leukemia viral oncogene homolog 4 (avian) CCDS6381.1NM_153831.2 FAK/PTK2 PTK2 protein tyrosine kinase 2 CCDS4098.1NM_005246.2 FER fer (fps/fes related) tyrosine kinase (phosphoproteinNCP94) CCDS10365.1 NM_002005.2 FES V-FES feline sarcoma viral/V-FPSfujinami avian CCDS6107.1 NM_023110.2 FGFR1 fibroblast growth factorreceptor 1 (fms- related tyrosine kinase 2, Pfeiffer syndrome)CCDS31298.1 NM_000141.3 FGFR2 fibroblast growth factor receptor 2(bacteria-expressed kinase, keratinocyte growth factor receptor)CCDS3353.1 NM_000142.2 FGFR3 fibroblast growth factor receptor 3(achondroplasia, thanatophoric dwarfism)William Allan Nix CCDS4410.1NM_002011.3 FGFR4 fibroblast growth factor receptor 4 isoform 1CCDS305.1 NM_005248.2 FGR Gardner-Rasheed feline sarcoma viral (v- fgr)oncogene homolog CCDS9330.1 NM_002019.3 FLT1/VEGFR1 fms-related tyrosinekinase 1 (vascular endothelial growth factor/vascular permeabilityfactor receptor) CCDS31953.1 NM_004119.2 FLT3 fms-related tyrosinekinase 3 CCDS4457.1 NM_182925.3 FLT4/VEGFR3 fms-related tyrosine kinase4 CCDS5103.1 NM_002031.2 FRK fyn-related kinase CCDS5094.1 NM_002037.3FYN FYN oncogene related to SRC, FGR, YES CCDS33460.1 NM_002110.2 HCKhemopoietic cell kinase CCDS10378.1 NM_000875.3 IGF1R insulin-likegrowth factor 1 receptor CCDS12176.1 NM_000208.2 INSR insulin receptorCCDS1160.1 NM_014215.1 INSRR insulin receptor-related receptorCCDS4336.1 NM_005546.3 ITK IL2-inducible T-cell kinase N/A NM_002227.2JAK1 Janus kinase 1 CCDS6457.1 NM_004972.2 JAK2 Janus kinase 2CCDS12366.1 NM_000215.2 JAK3 Janus kinase 3 CCDS3497.1 NM_002253.1KDR/VEGFR2 kinase insert domain receptor (a type III receptor tyrosinekinase) CCDS3496.1 NM_000222.2 KIT v-kit Hardy-Zuckerman 4 felinesarcoma viral oncogene homolog CCDS359.1 NM_005356.3 LCKlymphocyte-specific protein tyrosine kinase CCDS10078.1 NM_206961.1 LTKleukocyte tyrosine kinase CCDS6162.1 NM_002350.2 LYN v-yes-1 Yamaguchisarcoma viral related oncogene homolog CCDS12113.1 NM_002378.3 MATKmegakaryocyte-associated tyrosine kinase CCDS2094.1 NM_006343.2MERTK/MER c-mer proto-oncogene tyrosine kinase N/A NM_000245.2 MET metproto-oncogene (hepatocyte growth factor receptor) CCDS2807.1NM_002447.2 MST1R/RON macrophage stimulating 1 receptor (c-met- relatedtyrosine kinase) N/A NM_005592.1 MUSK muscle, skeletal, receptortyrosine kinase CCDS1161.1 NM_002529.3 NTRK1 neurotrophic tyrosinekinase, receptor, type 1 CCDS35053.1 NM_001007097.1 NTRK2 neurotrophictyrosine kinase receptor type 2 CCDS32322.1 NM_001012338.1 NTRK3neurotrophic tyrosine kinase receptor type 3 CCDS3495.1 NM_006206.3PDGFRA platelet-derived growth factor receptor alpha CCDS4303.1NM_002609.3 PDGFRB platelet-derived growth factor receptor betaCCDS4884.1 NM_002821.3 PTK7 PTK7 protein tyrosine kinase 7 CCDS6057.1NM_004103.3 PYK2/PTK2B PTK2B protein tyrosine kinase 2 beta CCDS7200.1NM_020975.4 RET ret proto-oncogene CCDS626.1 NM_005012.2 ROR1 receptortyrosine kinase-like orphan receptor 1 CCDS6691.1 NM_004560.2 ROR2receptor tyrosine kinase-like orphan receptor 2 CCDS5116.1 NM_002944.2ROS1 v-ros UR2 sarcoma virus oncogene homolog 1 (avian) N/ANM_001005861.2 RYK RYK receptor-like tyrosine kinase CCDS13294.1NM_005417.3 SRC v-src sarcoma (Schmidt-Ruppin A-2) viral oncogenehomolog (avian) CCDS13525.1 NM_080823.2 SRMS src-related kinase lackingC-terminal regulatory tyrosine and N-terminal myristylation sitesCCDS6688.1 NM_003177.3 SYK spleen tyrosine kinase CCDS3481.1 NM_003215.2TEC tec protein tyrosine kinase CCDS6519.1 NM_000459.2 TEK TEK tyrosinekinase, endothelial (venous malformations, multiple cutaneous andmucosal) CCDS482.1 NM_005424.2 TIE tyrosine kinase withimmunoglobulin-like and EGF-like domains 1 N/A NM_003985.3 TNK1 tyrosinekinase, non-receptor, 1 CCDS3480.1 NM_003328.2 TXK TXK tyrosine kinaseCCDS12236.1 NM_003331.3 TYK2 tyrosine kinase 2 CCDS10080.1 NM_006293.2TYRO3 TYRO3 protein tyrosine kinase CCDS11824.1 NM_005433.3 YES1 v-yes-1Yamaguchi sarcoma viral oncogene homolog 1 CCDS33254.1 NM_001079.3 ZAP70zeta-chain (TCR) associated protein kinase 70 kDa

Next, it was determined whether a mutation was somatic (i.e., tumorspecific) by examining the sequence of the gene in genomic DNA fromnormal tissue of the relevant patient. From the approximately 12 Mb ofsequence information obtained, 19 genes containing a total of 30 somaticmutations within their kinase domains were identified.

All coding exons of these 19 genes were then analyzed for mutations in atotal of 79 MM samples. The primers used for PCR amplification of ERBB4(CCDS accession CCDS2394.1; GenBank Accession No. NM_(—)005235.2; SEQ IDNO: 1) are listed in Table 3. ERBB4 was sequenced using the followingprimers:

Forward - TGTAAAACGACGGCCAGT (SEQ ID NO: 78) Reverse -CAGGAAACAGCTATGACC (SEQ ID NO: 79)

TABLE 3 Primers used for PCR amplification of the ERBB4 kinase domainERBB4 SEQ ID SEQ ID Exon Forward Primer NO: Reverse Primer NO: Exon 18TCATTTGTGCAGCAACTTC 64 CTGTCCTAGGGTTTTGGC 71 TC ATT Exon 19GCAGACAGTTGTGAAGCA 65 TGCTATCCTATTTCCATG 72 AAAG CTGT Exon 22CAAGCTTTAATTCGCAAA 66 TCCCCACTTAATTATTTT 73 GAAGA TACCTTT Exon 22TGCTTTAGGAAATTAGGC 67 GGCTACTCAGAGGCTAA 74 TTATC GGTG Exon 23TTTTTCCTTCATGTTTAGA 68 TTTTTAATTGATTGGTGT 75 TCATTT TTGG Exon 23ACCTTGTCCTGCTAATTTG 69 TGACCTGTAAGGAGTAT 76 CTC TCTTTTACTAC Exon 24CAGTAGCAGAGCCACTTG 70 TGTCCACCAGGACAAAT 77 AA GTA

Through this approach, 99 non-synonymous mutations were identified in 19genes (Table 4, FIGS. 4A-4B and FIG. 5). All of these mutations wereshown to be somatic by sequencing of DNA from matched normal tissue.Only three genes (EPHA6, PDGFRA and PTK2) out of the 19 had previouslybeen reported to be mutated in MM (see Cancer Gene Census, availableonline at www.sanger.ac.uk/genetics/CGP/Census/). The majority of tumorswith PTK gene mutations also contained mutations in NRAS or BRAF (Table4).

TABLE 4 Somatic mutations identified in PTKs CCDS Ref Seq No. % of casesGene Other names accession* accession* of mutations# affected # DDR1CAK, CCDS4690.1 NM_001954.3 2 2.6 CD167 EDDR1, NEP, NTRK4 PTK3A, RTK6FER TYK3 CCDS4098.1 NM_005246.1 2 2.6 FLT1 FLT CCDS9330.1 NM_002019.3 810.3 VEGFR1 EPHA6 FLJ35246 NM_001080448.2 5 6.4 EPHA10 FLJ16103CCDS41305.1 NM_001099439.1 7 6.4 FLJ33655 EPHB1 EPHT2 NM_004441 4 5.1Hek6 EPHB2 DRT CCDS229.2 NM_017449.1 7 9.0 EPHT3 ERK Hek5 Tyro5 EPHB6HEP CCDS5873.1 NM_004445.1 7 9.0 ERBB4 HER4 CCDS2394.1 NM_005235.2 2418.8 MGC138404 p180erbB4 MATK CTK CCDS12113.1 NM_002378.2 1 1.3 HYLTKMET HGFR CCDS43636.1 NM_000245 3 3.8 NTRK1 MTC CCDS1161.1 NM_002529.2 22.6 TRK PDGFRA TRKA CCDS3495.1 NM_006206.2 5 5.1 CD140a PDGFR2 PTK2 FAK,CCDS6381.1 NM_153831.2 1 1.3 FADK FAK1, pp125FAK PTK2B PYK2 CCDS6057.1NM_173176.1 8 10.0 PKB PTK CAKB FAK2 FRNK CADTK FADK2 PTK6 RAFTKCCDS13524.1 NM_005975.2 2 2.6 BRK PTK7 CCK4 CCDS4884.1 NM_002821.3 1 1.3ROR2 BDB CCDS6691.1 NM_004560.2 4 5.1 BDB1 NTRKR2 TIE1 JTK14 CCDS482.1NM_005424.2 6 7.7 TIE NRAS/ Functional BRAF Gene Exon Nucleotide† AminoAcid† Domain Tumor mutation** DDR1 8 C1115T S372F None 6T BRAF 11 G1709AR570Q Protein 43T BRAF Tyrosine Kinase FER 11 T1594C Y532H SH2 Motif 58TBRAF 13 G1739A G580D Protein 30T BRAF Tyrosine Kinase FLT1 7 G842A R281QIG 37T BRAF 7 C860T S287F IG 7T NRAS 12 −9 Intronic Splice N/A 20T BRAFC > A Site 13 G1767A W589X IGc2 13T None 17 C2440T P814S None 39T None21 G2827A E943K Protein 44T NRAS Tyrosine Kinase 24 G3241A D1081NProtein 78T BRAF Tyrosine Kinase 28 G3667A E1223K/ None 85T BRAF LOHEPHA6 1 C1202G T307S None 30T BRAF 4 G1763T R494M Protein 36T BRAFTyrosine Kinase 4 G1891A E537K Protein 32T BRAF Tyrosine Kinase 8 A2246TK655I Protein 29T BRAF Tyrosine Kinase 8 G2320A E680K None 21T BRAFEPHA10 3 G235A V79M Ephrin 52T BRAF Receptor 3 T236C V79A Ephrin 52TBRAF Receptor 3 G370A E124K Ephrin 55T None Receptor 3 G649A G217S None71T BRAF 3 G650A G217D None 71T BRAF 13 G2369A G790E Protein 63T NRASTyrosine Kinase 14 G2528C G843A Protein 37T BRAF Tyrosine Kinase EPHB1 3C235T R79W Ephrin 39T None Receptor 12 G2311A D771N Protein 60T NRASTyrosine Kinase 13 G2432A G811E Protein 44T NRAS Tyrosine Kinase 15G2757A W919X Sterile Alpha 63T NRAS Motif EPHB2 3 G325A E109K Ephrin 4TBRAF Receptor 3 C614T A205V None 72T None 4 G952A D318N Fibronectin 71TBRAF Type 3 Domain 7 C1535T T512I Fibronectin 83T Both Type 3 Domain 10G1846A E615K Protein 29T BRAF Tyrosine Kinase 10 G1846A E615K Protein68T BRAF Tyrosine Kinase 14 C2663T P887L None 77T None EPHB6 3 C392TS131F Ephrin 60T NRAS Receptor 3 C455T S152F Ephrin 55T None Receptor 5G1210A G404S Fibronectin 50T BRAF Type 3 Domain 11 G2036A R679Q Protein5T BRAF Tyrosine Kinase 11 C2063G A688G Protein 54T BRAF Tyrosine Kinase11 C2110T R704W Protein 26T BRAF Tyrosine Kinase 13 −5 Intronic SpliceN/A 18T None C > T Site ERBB4 2 C113T L39F Receptor L 71T BRAF Domain 3T331C Y111H Receptor L 13T None Domain 8 G939A M313I Growth Factor 63TNRAS Receptor 8 G949A E317K Growth Factor 17T NRAS Receptor 9 C1022TS341L Receptor L 96T None Domain 10 C1177T R393W Receptor L 49T BRAFDomain 11 C1226T P409L Receptor L 76T None Domain 12 G1354A E452KReceptor L 7T NRAS Domain 12 G1354A E452K/ Receptor L 55T None LOHDomain 12 G1472A R491K/ Growth Factor 34T BRAF LOH Receptor 14 G1624AE542K Growth Factor 63T NRAS Receptor 14 C1630T R544W Growth Factor 56TBRAF Receptor 14 G1687A E563K Growth Factor 12T NRAS Receptor 15 −10Splice N/A 68T BRAF Intronic Site/ C > T LOH 15 G1825A D609N GrowthFactor 76T None Receptor 18 C2098T P700S None 24T NRAS 21 G2506A E836KProtein 86T BRAF Tyrosine Kinase 21 G2614A E872K Protein 63T NRASTyrosine Kinase/Activation Loo 23 G2806A G936R Protein 24T NRAS TyrosineKinase 24 −4 Intronic Splice N/A 13T None C > T Site 25 C3097T P1033SNone 76T None 26 −1 Intronic Splice N/A 76T None G > A Site 28 G3521AR1174Q None 63T NRAS 28 G3737A S1246N His-Me Finger 71T BRAFEndonucleases MATK 12 G1248A W416X Protein 13T None Tyrosine Kinase MET5 G1829A C610Y/ IPT 1T BRAF LOH 14 A3176G N1059S None 13T None 16 G3509AR1170Q Protein 29T BRAF Tyrosine Kinase NTRK1 8 G1137A M349I None 18TNone 14 C1747G R547G Protein 13T None Tyrosine Kinase PDGFRA 3 G571AA191T IG 64T BRAF 9 G1375A E459K/ None 32T BRAF LOH 18 C2669T S890FProtein 41T BRAF Tyrosine Kinase 20 C2810T P937L/ Protein 32T BRAF LOHTyrosine Kinase 21 G3070A D1024N None 63T NRAS PTK2 15 C1481T A494VProtein 13T None Tyrosine Kinase PTK2B 5 −4 Intronic Splice N/A 79T BRAFC > T Site 8 G818A W273X FERM 76T None 13 G1241A G414E None 95T NRAS 14C1285T R429C Protein 17T NRAS Tyrosine Kinase 16 G1480A E494K Protein26T BRAF Tyrosine Kinase 24 G2374A E792K None 36T BRAF 29 G2753A R918QFocal AT 85T BRAF 29 G2812A E938K Focal AT 83T Both PTK6 4 G629A W210XProtein 12T NRAS Tyrosine Kinase 5 −7 Intronic Splice N/A 51T BRAF C > TSite PTK7 7 C1054T P352S IGc2 84T BRAF ROR2 5 T574C Y192H Frizzled 71TBRAF Cysteine-Rich Domain 7 T1172C V391A Kringle 72T None 9 C1670T S557LProtein 5T BRAF Tyrosine Kinase 9 G2377T A793S None 81T BRAF TIE1 2G139A E47K None 13T None 2 C161T S54L None 16T BRAF 2 C266T T89M None52T BRAF 2 G292A D98N None 43T BRAF 11 G1598A G533E Fibronectin 39T NoneType 3 Domain 22 C3281T P1094L/ Protein 12T NRAS LOH Tyrosine Kinase*Accession numbers for mutated PTKs in Santa Cruz and GenBank. # Numberof non-synonymous and splice site mutations observed and percent oftumors affected for each of the 19 genes in the panel of 80 melanomacancers. †Nucleotide and amino acid change resulting from mutation. “X”refers to stop codon. “LOH” refers to cases wherein the wild-type allelewas lost and only the mutant allele remained. “Splice site” refers to acase wherein the alteration affected ten bases spanning the exon.**Mutations previously observed in NRAS, or BRAF. “None” refers to nomutation observed. SH2 Motif, Src homology 2 domain; IG, Immunoglobin;IGc2, Immunoglobin C-2 Type; IPT, IG-like, p1exins, transcriptionfactors; Focal AT, Focal Adhesion Targeting Region; FERM, Protein 4.1,Ezrin, Radixin, Moesin Domain. Domains were found using Ensembl andInterPro.

The observed somatic mutations could either be “driver” mutations thatplay a functional role underlying the neoplastic process ornonfunctional “passenger” changes. In the 19 genes found to be mutated,99 non-synonymous and 17 synonymous somatic mutations were identified,yielding a N:S (non-synonymous:synonymous) ratio of 99:17, significantlyhigher than the N:S ratio of 2.5:1 predicted for nonselected passengermutations (P<1×10⁻⁵) (Sjoblom et al., Science 314:268-274, 2006),suggesting that these are likely to be “driver” mutations. The number ofC>T mutations was significantly greater than other nucleotidesubstitutions resulting in a high prevalence of C:G>T:A transitions(p<0.0001) (FIG. 6A), confirming previously reported melanomasignatures. A summary of the most highly mutated genes is shown in FIG.5.

Example 3 Somatic Mutations within ERBB4 are Frequent in MM

This example describes the biochemical analysis of several ERBB4mutations identified in patients with melanoma. To evaluate the effectof some of these mutations on kinase function, the studies describedherein focus on ERBB4, a member of the EGFR kinase subfamily, which wasthe most highly mutated gene (19%) in the screen. Five of the 15 sampleswith ERBB4 mutations contained more than one somatic mutation in ERBB4,which may act synergistically as previously seen for EGFR (Godin-Heymannet al., Cancer Res. 67:7319-7326, 2007). The large number of mutationsobserved in ERBB4 strongly suggests that these mutations arefunctionally important (FIG. 1A). This conclusion is supported byanalysis of the ratio of non-synonymous to synonymous mutations inERBB4, which was 24:3, significantly higher than the 2.5:1 ratioexpected by chance (P<1×10⁻²) (Sjoblom et al., Science 314:268-274,2006).

Interestingly, 7 out of the 24 non-synonymous somatic mutationsdiscovered in ERBB4 occurred at Glu (E) residues (p<0.00005, binomialtest), all of which resulted in changes to Lys (K), causing a chargereversal. The underlying reason for this might be due to the highfrequency of C:G>T:A transitions (FIG. 6B). Clustering of somaticmutations is seen in various functional domains of ERBB4 (FIG. 1A andFIG. 5), with mutations in the kinase domain co-localizing withpreviously described mutations (found in various cancer types atfrequencies ranging from 1.1-4.7%; Soung et al., Int. J. Cancer118:1426-1429, 2006; Ding et al., Nature 455:1069-1075, 2008) andoccurring at highly conserved residues. These genetic data suggest thatmutant ERBB4 is likely to function as an oncogene in melanoma.

The positions of these mutations within ERBB4 and their predominantlyheterozygous nature imply that they are likely to be gain of functionmutations. No truncating mutations were observed and the alterationsoccurred in functionally important domains (FIG. 1A). The affectedresidues in ERBB4 are highly conserved evolutionarily, retainingidentity in chimp, horse, rat, mouse and opossum. Clustering of somaticmissense mutations is seen in various domains. Mutations S341L, R393W,P409L, E452K and R491K all occur in the extracellular sub region III,with the E452K mutation occurring in two different cases. MutationsE542K, R544W and E563K are all adjacent in the extracellular sub regionIV. A similar clustering was observed in the kinase domain where ournovel mutations co-localized with previously described mutations (foundin various cancer types at frequencies ranging from 1.1%-4.7% (Ding etal., Nature 455:1069-1075, 2008; Soung et al., Int. J. Cancer118:1426-1429, 2006). The clustering of somatic missense mutations inspecific domains of ERBB4 is similar to that observed for activatingmutations in other oncogenes, such as BRAF and PIK3CA (Davies et al.,Nature 417(6892):949-954, 2002; Samuels et al., Science 304:554, 2004).These genetic data suggest that mutant ERBB4 is likely to function as anoncogene in MM.

Example 4 ERBB4 Mutations Increase its Kinase Activity

This example describes the assessment of kinase activity of ERBB4mutations present in melanoma tumors. To directly test whether themutations identified in ERBB4 activate its kinase activity, thepositions of the various ERBB4 missense mutations in its crystalstructure were assessed. The crystal structures of the extracellular andkinase domains of ERBB4 (Bouyain et al., Proc. Natl. Acad. Sci. USA102:15024-15029, 2005; Qiu et al., Structure 16:460-467, 2008)demonstrated that most of the observed alterations had similarpositioning to mutations reported in the ERBB4 family members EGFR andERBB2 in lung cancer, glioblastoma and gastric cancer (Riese et al.,Bioessays 29:558-565, 2007). The mutations that were further evaluatedin the extracellular domain included the E317K mutation, which is nearthe EGFR

R324L mutation, the E542K, R544W, and E563K mutations, as theseco-localize, and finally the E452K mutation, as this substitutionoccurred in two patients. Additionally, two mutations that were found inthe kinase domain were cloned: E836K, which is found near the ERBB2N857S mutation, and the E872K alteration.

To investigate the biochemical effects of the identified ERBB4mutations, wild type (WT) ERBB4 or the seven mutants (E317K, E452K,E542K, R544W, E563K, E836K, E872K), as well as a kinase dead (KD)version of ERBB4 (K751M), were transiently expressed in HEK 293T cellsand the basal catalytic activity of ERBB4 was assessed using ERBB4autophosphorylation as a readout for receptor activation. ERBB4autophosphorylation was determined by measuring the totalphosphotyrosine content of the immunoprecipitated receptor as well as bymeasuring two auto-phosphorylation sites (Tyr-1162 and Tyr-1284) in theC-terminus of ERBB4. Compared to WT ERBB4, all the missense mutantsshowed a marked increase in receptor autophosphorylation on totalphosphotyrosine as well as on residues Tyr-1162 and Tyr-1284 (FIG. 1B).No site-specific phosphorylation was observed in cells exogenouslyexpressing the KD version of ERBB4. Similar expression levels of totalERBB4 protein were observed, except KD ERBB4, which had a higherexpression level (FIG. 1B).

The specificity of the phosphosite-specific anti-ERBB4 antibodies wasconfirmed using competitive ERBB4-phosphosite-specific phospho-peptides(FIG. 7). To assess whether the increased tyrosine phosphorylation ofthe ERBB4 mutants correlates with increased kinase activity, a kinaseassay using the same set of ERBB4 mutants was performed. FIGS. 1C-1Dshow that in low serum, the ERBB4 mutants exhibit a marked increase inkinase activity compared to WT ERBB4. In contrast, in the presence ofserum, the ERBB4 mutants showed a similar kinase activity compared to WTERBB4. Similar expression levels of total ERBB4 protein were observed(FIG. 1D). These results suggest that increased ERBB4 phosphorylation isdue to its constitutive activation rather than alteration in its proteinlevels.

To extend these observations, a MM line containing endogenous mutantERBB4 (63T, E542K/E872K) was studied and compared it to a MM linecontaining endogenous WT ERBB4 (39T). As in transfected cells, ERBB4autophosphorylation was markedly elevated in the MM line with anendogenous ERBB4 mutation (FIG. 8).

To determine if the increased tyrosine phosphorylation of the ERBB4mutants correlates with increased kinase activity, a kinase assay usingthe same set of ERBB4 mutants was performed. The ERBB4 mutants showed amarked increase in kinase activity compared to WT ERBB4 and expressionlevels of total ERBB4 protein were comparable (FIG. 1E). As intransfected cells, ERBB4 autophosphorylation was markedly elevated inthe melanoma lines harboring ERBB4 mutations compared to melanoma linesharboring endogenous WT ERBB4 (FIGS. 1F-1G).

ERBB4 is known to activate several downstream signaling pathwaysincluding the ERK and AKT pathways (Frey et al., Gastroenterology136:217-226, 2009). To evaluate which of these signaling pathways isactivated by the ERBB4 mutations, immunoblot analysis of melanoma celllines harboring endogenous ERBB4 mutations was performed.Phosphorylation of AKT was elevated in cells expressing any of the threeevaluated mutant ERBB4s, whereas ERK showed similar activation in cellsexpressing WT or mutant ERBB4 (FIG. 11).

Example 5 ERBB4 Mutations Promote Colony Formation Abilities andAnchorage-Independent Growth

The example describes the phenotypic analysis of ERBB4 mutantsidentified in melanoma tumors. The combination of biochemical andgenetic data disclosed herein suggested that the mutant ERBB4 proteinsmight be oncogenic. However, previous studies have described thegeneration of ERBB4 mutants that are constitutively active butnon-transforming (Penington et al., Cell Growth Differ. 13:247-256,2002; Williams et al., Cancer Lett. 192:67-74, 2003). Thus, thefollowing studies were performed to determine whether the melanoma ERBB4variants described in this study are transforming. To test this, NIH 3T3cells were transiently transfected with vector, WT, one of the sevenconstitutively active ERBB4 mutants (E317K, E452K, E542K, R544W, E563K,E836K and E872K) or oncogenic K-Ras^(G12v). Ten days after transfection,all ERBB4 mutations transformed NIH 3T3 cells more efficiently than WTERBB4. Strikingly, the transformation ability of the ERBB4 mutants wassimilar to oncogenic K-Ras^(G12V) (FIG. 2A). Similarly, the same set ofERBB4 mutants were able to promote anchorage-independent growth asdepicted in FIG. 9A. All the presented results were significant (P<0.05,t test).

To test the transformation abilities of the ERBB4 mutations in humanmelanoma cells, stable cell pools expressing vector, WT, and three ERBB4mutations (E452K, E563K and E872K) were derived in SK-MeI-2 cells, amelanoma cell line that expresses WT ERBB4. Western blot analysis showeda similar expression level of ERBB4 in all clones (FIG. 9B). As seen inFIG. 2B, expression of all the ERBB4 mutants elicited a significantlyhigher cell transformation ability compared to clones expressing vectoror WT ERBB4 (p<0.05, t-test). When the same set of clones was suspendedin soft agar, cells expressing mutant ERBB4 formed a significantlyhigher number of anchorage-independent colonies (p<0.05, t-test, FIG.9C). Thus, all the tested ERBB4 mutants potently increased both colonyformation ability as well as growth on soft agar in all the cell linescompared to vector or WT ERBB4 stable clones.

Example 6 Dependency of MM Lines Harboring ERBB4 Mutations on ERBB4Signaling

This example describes the effect of inhibiting expression of WT andmutant ERBB4 using shRNA. In order to assess if melanoma cells harboringendogenous ERBB4 mutations are dependent on ERBB4 signaling forproliferation, short hairpin RNA (shRNA) was used to stably knockdownERBB4 protein levels in melanoma lines harboring either WT (2T and 31T)or mutant ERBB4 (17T, E317K; 63T, E542K/E872K; or 7T, E452K). Specifictargeting of ERBB4 by shRNAs was confirmed both in transfected HEK 293cells and in one of the melanoma cell lines by immunoblotting (FIGS.3A-3B). Three unique shRNA constructs targeting ERBB4 had minimal effecton the proliferation of cells expressing WT receptor, but significantlyreduced the growth of melanoma lines containing mutant ERBB4 (FIGS.3C-3G). Thus, mutant ERBB4 is essential for growth of melanomasharboring these mutations. Evaluation of the effects of ERBB4 knockdownon downstream signaling pathways revealed that down-regulation of ERBB4in cells harboring mutant versions of the gene reduces levels ofendogenous, phosphorylated AKT, but not of phosphorylated ERK. Incontrast, inhibition of ERBB4 expression in cells harboring WT versionsof the gene showed similar levels of AKT and ERK activation (FIG. 12).

Because shRNA-mediated cell death could result from specific ornonspecific effects, an exogenous, non-targetable WT ERBB4 construct (NTERBB4), engineered to be resistant to knockdown by the introduction ofthree silent mutations in the region of ERBB4 targeted by shRNA #6, wasexamined for the ability to rescue the effects of knockdown ofendogenous ERBB4. Melanoma cells harboring the E317K mutation stablyexpressing either control or ERBB4 shRNA #6 construct were transducedwith the lentiviral NT ERBB4 construct or empty vector as control.Similar phosphotyrosine content is observed in both WT and NT ERBB4constructs, demonstrating that the silent mutations in the NT constructdo not affect the ability of the receptor to be phosphorylated towild-type levels (FIG. 13A). Importantly, pooled clones of NTreconstituted cells were markedly more resistant to growth inhibitioninduced by ERBB4 knockdown (#6/NT) than shRNA control-infected cells(Vect/Vect).

To evaluate mutant ERBB4 as a potential target for specific inhibitionof melanoma cell survival, the ERBB4 pathway was targeted with theFDA-approved pan-ERBB pharmacologic inhibitor, lapatinib (GW2016)(Heymach et al., Clin. Cancer Res. 12:4441s-4445s, 2006). Exposure ofmelanoma cells to lapatinib resulted in reduced cell proliferation to agreater extent in cells containing endogenous ERBB4 mutations than incells containing endogenous WT ERBB4 (FIG. 10A). An IC₅₀ calculationrevealed that melanoma cells harboring ERBB4 mutations were 10- to250-fold more sensitive to lapatinib than cells with WT receptor (FIG.10B) and treatment with lapatinib inhibited receptor autophosphorylationin a dose-dependent manner (FIG. 10C). This increased sensitivity tolapatinib was accompanied by specific inhibition of ERBB4 and AKTactivation in cells harboring mutant ERBB4 (FIGS. 10D-10E). Activationof other downstream elements, such as ERK, was also slightly inhibitedby lapatinib (FIGS. 14A-14B). Thus, although signaling by mutant ERBB4demonstrates selective activation of AKT, lapatinib treatment of cellsharboring mutant ERRB4 results in uniform inhibition of downstreamsignaling pathways. Only mutant ERBB4 was inhibited by lapatinib in themelanoma cell lines. No inhibition of its family member ERBB2 wasobserved (FIGS. 10D-10E) and no phosphorylation of EGFR was observed inany of these cells. The observed reduced proliferation occurred in cellsharboring BRAF, NRAS, ARAF or CRAF mutations in addition to the ERBB4mutations.

TABLE 5 Mutations identified in RAF and RAS isoforms Sample ERBB4 BRAFNRAS ARAF CRAF HRAS KRAS  7T E452K wt Q61R wt wt wt wt 12T E563K wtQ61Q/R wt wt wt wt 17T E317K wt Q61Q/K wt wt wt wt 31T wt wt wt wt wt wtwt 34T R491K V600V/E wt wt T362T/A wt wt 39T wt wt wt wt wt wt 49TR393R/W V600V/E wt wt wt wt wt 55T E452K V600V/E wt P216S wt wt wt P254L56T R544R/W V600V/E wt wt wt wt wt 63T E542K wt Q61Q/K wt wt wt wt E872K68T Splice site V600V/E wt wt wt wt wt LOH 71T L39L/F V600V/M wt wt wtwt wt S1246S/N V600V/E 86T E836E/K V600V/E wt wt wt wt wt 93T wt wt wtA345A/G wt wt wt

To elucidate the mechanism of decreased growth of cells expressingmutant ERBB4 following lapatinib treatment, cells were examined for cellcycle perturbations or apoptosis by flow cytometry. Lapatinib markedlyincreased apoptosis of melanoma cells harboring mutant ERBB4 compared tolines harboring WT ERBB4 (FIGS. 10E-10G). Thus, expression of mutantERBB4 appears essential for suppression of pro-apoptotic signals inmelanoma cells harboring these mutations, which is consistent with theselective activation of AKT in ERBB4 mutant cells (FIGS. 11A-11B) andprevious results demonstrating an anti-apoptotic role for AKT (Grant etal., Front. Biosci. 7:d76-89, 2002). These results suggest thatlapatinib preferentially inhibits mutant ERBB4 signaling and that cellswith ERBB4 mutations are subject to “oncogene addiction” (Weinstein,Science 297:63-64, 2002). Moreover, the enhanced AKT signaling in cellswith mutant ERBB4 may provide an additional therapeutic target in thesetumors.

In view of the many possible embodiments to which the principles of thedisclosed invention may be applied, it should be recognized that theillustrated embodiments are only preferred examples of the invention andshould not be taken as limiting the scope of the invention. Rather, thescope of the invention is defined by the following claims. We thereforeclaim as our invention all that comes within the scope and spirit ofthese claims.

1. A method of detecting a mutation in the ERBB4 gene that is associatedwith a poor prognosis of a subject diagnosed with melanoma, comprisingdetecting the presence of a mutation in the ERBB4 gene in a melanomasample from the subject, wherein the mutation is selected from G949A,G1354A, G1624A, C1630T, G1687A, G2506A and G2614A (numbered withreference to SEQ ID NO: 1).
 2. The method of claim 1, wherein the poorprognosis is an increase in the likelihood of death.
 3. The method ofclaim 1, wherein the poor prognosis is an increase in the likelihood ofmetastasis.
 4. The method of claim 1, wherein the mutation in the ERBB4gene results in an increase in kinase activity of the ERBB4 protein. 5.The method of claim 1, further comprising obtaining the melanoma samplefrom the subject.